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dwca.rb
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module BatchLoad
# TODO: Originally transliterated from Import::CollectingEvents: Remove this to-do after successful operation.
class Import::DWCA < BatchLoad::Import
attr_accessor :collecting_events
attr_accessor :dwca_namespace
attr_accessor :repo
attr_accessor :parser
attr_accessor :tasks_
attr_accessor :rows
attr_accessor :row_objects
# @param [Hash] args
def initialize(dwca_namespace: nil, **args)
@dwca_namespace = dwca_namespace
@root = args.delete(:root)
@kingdom = args.delete(:kingdom)
@cat_no_pred = args.delete(:cat_no_pred)
@geo_rem_kw = args.delete(:geo_rem_kw)
@repo = args.delete(:repo)
@namespace = args.delete(:namespace)
@collecting_events = {}
@rows = {}
@row_objects = {}
@parser = ScientificNameParser.new
@tasks_ = {
make_ident: %w(catalognumber occurrenceid),
make_prsn: %w(georeferencedby),
make_tn: %w(scientificname taxonrank family kingdom),
make_td: %w(scientificname basisofrecord individualcount organismquantity organismquantitytype recordedby),
# make_otu: %w(scientificname),
make_co: %w(individualcount organismquantity organismquantitytype),
make_ba: %w(associatedtaxa),
make_notes: %w(georeferenceremarks locationremarks occurrenceremarks),
make_tag: %w(),
make_gr: %w(decimallatitude decimallongitude countrycode stateprovince county municipality locality coordinateuncertaintyinmeters georeferencedby),
make_ce: %w(decimallatitude decimallongitude coordinateuncertaintyinmeters eventdate locationremarks recordedby geodeticdatum countrycode stateprovince county municipality locality)
}.freeze
super(args)
end
# @return [Hash]
def preview_dwca
@preview_table = {}
@preview_table
end
=begin Headers from PSUC DWCS
catalogNumber
scientificName
taxonRank
family
kingdom
individualCount
organismQuantity
organismQuantityType
basisOfRecord
eventDate
recordedBy
verbatimLocality
locationRemarks
associatedTaxa
occurrenceRemarks
countryCode
stateProvince
county
municipality
locality
decimalLatitude
decimalLongitude
coordinateUncertaintyInMeters
georeferencedBy
georeferenceProtocol
georeferenceRemarks
geodeticDatum
collectionID
occurrenceID
=end
# process each row for information:
# rubocop:disable Metrics/MethodLength
# rubocop:disable Metrics/BlockNesting
# @return [Integer]
def build_dwca
line_counter = 1 # accounting for headers
tasks = triage(csv.headers, tasks_)
csv.each do |row|
@warns = []
@errs = []
@rows[line_counter] = {}
@rows[line_counter][:row] = row
@row_objects = {}
tasks.each {|task|
results = send(task, row)
@row_objects[task] = results
warn = results[:warn]
err = results[:err]
@errs.push(results.delete(:err)) unless err.blank?
@warns.push(results.delete(:warn)) unless warn.blank?
}
t_n = @row_objects[:make_tn].select {|kee, val| val != nil}.values.first
# save the (possible new) taxon_name
t_n.save! if t_n.new_record?
# associate the taxon_name with the otu
otu = Otu.find_or_create_by!(taxon_name: t_n)
otu.save! if otu.new_record?
@row_objects[:make_otu] = otu
t_d = @row_objects[:make_td]
c_o = @row_objects[:make_co][:c_o]
idents = @row_objects[:make_ident]
id_cat_no = idents[:id_cat_no]
id_occ_id = idents[:id_occ_id]
b_a_s = @row_objects[:make_ba]
notes = @row_objects[:make_notes]
c_o_notes = notes[:c_o]
c_e_notes = notes[:c_e]
g_r_notes = notes[:g_r]
c_e = @row_objects[:make_ce][:c_e]
g_r = @row_objects[:make_gr]
ppl = @row_objects[:make_prsn]
unless c_e.valid?
test_list = c_e.errors.keys
if test_list.include?(:start_date_day) or
test_list.include?(:start_date_month) or
test_list.include?(:start_date_year) or
test_list.include?(:end_date_day) or
test_list.include?(:end_date_month) or
test_list.include?(:end_date_year)
@warns.push(c_e.errors.full_messages)
@warns.push("eventDate (#{c_e.verbatim_date}) does not parse properly.")
c_e.start_date_day = nil
c_e.start_date_month = nil
c_e.start_date_year = nil
c_e.end_date_day = nil
c_e.end_date_month = nil
c_e.end_date_year = nil
end
end
if c_e.valid? # check c_e again
c_e.save if c_e.new_record?
unless c_e_notes.blank?
apply_note = false
c_e_notes.each_key {|kee|
c_e_n = c_e_notes[kee]
if c_e.notes.present?
c_e.notes.each {|note|
if note.text == c_e_n.text
# need to drop the object without warning
@row_objects[:make_notes][:c_e].delete(:remark)
else
apply_note = true
end
}
else
apply_note = true
end
c_e_n.note_object = c_e if apply_note
}
end
else
@errs.push(c_e.errors.full_messages.flatten)
# everything else is a fail.
line_counter = loop_end(line_counter)
next
end
# associate the collection_object with the collecting_event
c_o.collecting_event = c_e
# associate the namespace and catalog number with the collection_object
if id_cat_no.blank?
@warns.push('Missing catalog number.')
else
c_o.identifiers << id_cat_no
end
if id_occ_id.blank?
# is a warning required?
else
c_o.identifiers << id_occ_id
end
c_o.repository = @repo
c_o.save!
# add the possible biological_associations, new? otu to collection_object
unless b_a_s.blank?
b_a_s.each_key {|kee|
b_a = b_a_s[kee]
b_a.biological_association_subject = c_o
}
end
# add notes to collection_object, if required
unless c_o_notes.blank?
c_o_notes.each_key {|kee|
c_o_notes[kee].note_object = c_o
}
end
# associate the collection_object with the otu using the taxon_determiniation
t_d.biological_collection_object = c_o
t_d.otu = otu
t_d.save!
# associate the georeference with the collecting_event
g_r.collecting_event = c_e
# two different types of georeferences: verbatim, and geolocate
if g_r.type.include?('Ver')
# for verbatim_data, generate a new georeference using the collecting_event
a = c_e.generate_verbatim_data_georeference
if a.valid?
# and replace the pre-built georeference
g_r = c_e.georeferences.last
@row_objects[:make_gr] = g_r
else
@warns.push(a.errors.full_messages)
@row_objects.delete(:make_gr)
end
else
# is a GeoLocate
unless g_r.valid?
# georeference was (0,0), will be dropped
err_txt = 'Georeference::GeoLocate cannot be created, '
if g_r.errors.messages[:collecting_event_id].present?
# what to do here?
@warns.push(err_txt + 'duplicate georeference')
else
@warns.push(err_txt + 'lat/long not valid.')
end
@row_objects.delete(:make_gr)
unless g_r_notes.blank?
@warns.push('Georeference::GeoLocate cannot be created, \'georeferenceRemark\' has been dropped.')
@row_objects[:make_notes].delete(:g_r)
end
end
end
# add a georeferencer as required
g_rer = ppl[:g_r]
unless g_rer.blank?
unless g_r.georeferencers.include?(g_rer)
g_r.georeferencers << g_rer
end
end
# add notes to georeference, if required
unless g_r_notes.blank?
apply_note = false
g_r_notes.each_key {|kee|
g_r_n = g_r_notes[kee]
if g_r.notes.present?
g_r.notes.each {|note|
if note.text == g_r_n.text
# need to drop the object without warning
@row_objects[:make_notes][:g_r].delete(:remark)
else
apply_note = true
end
}
else
apply_note = true
end
g_r_n.note_object = g_r if apply_note
}
end
# either the original, or the ce-created one gets saved
# g_r.save
begin # make sure all objects for this row get saved
@row_objects.each_key {|kee|
objects = @row_objects[kee]
case objects.class.to_s
when 'Array'
objects.flatten.each {|object|
if object.valid?
object.save
else
@errs.push(object.errors.full_messages)
end
}
when 'Hash'
@errs.push(save_hash(objects))
else # all other single object classes
test = objects.try(:valid?)
case test
when true
objects.save
when false
@errs.push(objects.errors.full_messages)
when nil
@warns.push('No georeference exists.')
end
end
}
#@warns.push("warning #{line_counter}")
#@errs.push("error #{line_counter}") if line_counter.even?
@warns.flatten!
@errs.flatten!
# ap@warns
end
line_counter = loop_end(line_counter)
# break if line_counter > 30
end
@total_lines = line_counter - 1
end
# rubocop:enable Metrics/MethodLength
# rubocop:enable Metrics/BlockNesting
# @return [Boolean]
def build
if valid?
build_dwca
@processed = true
end
end
def create
end
private
# package up the results of the process into a hash
# @param [Integer] line_counter current line_counter/rows key
# @return [Integer] new line_counter/rows key
def loop_end(line_counter)
@rows[line_counter][:row_objects] = @row_objects
@rows[line_counter][:err] = @errs
@rows[line_counter][:warn] = @warns
line_counter + 1
end
# @param [Hash] objects
def dump_hash(objects)
objects.each_key {|kee|
object = objects[kee]
unless object.blank?
if object.class.to_s == 'Hash'
dump_hash(object)
else
object.destroy
end
end
}
end
# @param [Hash] objects
# @return [Array]
def save_hash(objects)
l_errs = []
objects.each_key {|kee|
object = objects[kee]
unless object.blank?
if object.class.to_s == 'Hash'
l_errs.push(save_hash(object))
else
if object.valid?
object.save
else
l_errs.push(object.errors.full_messages)
end
end
end
}
l_errs.flatten
end
# only for use in a TaxonWorks rails console
def _setup
$project = Project.where(name: 'BatchLoad Test').first
$project_id = $project.id
$user = User.find(185)
$user_id = $user.id
@root = Protonym.find_or_create_by(name: 'Root',
rank_class: 'NomenclaturalRank',
parent_id: nil,
project_id: $project_id)
@animalia = Protonym.find_or_create_by(name: 'Animalia',
parent_id: @root.id,
rank_class: Ranks.lookup(:iczn, :kingdom),
project_id: $project_id)
end
# @param [CSV::Row] row
# @return [Hash]
def make_ba(row)
# for each associatedTaxa, find or create an otu, and creata a biological association for it,
# connecting it to a collection_object
retval = {}
bas = row['associatedtaxa']
unless bas.blank?
taxa = bas.split('|')
taxa.each {|bio_assoc|
unless bio_assoc.blank?
br = BiologicalRelationship.find_or_create_by!(name: 'associated_taxa',
project_id: @project_id)
otu = Otu.find_or_create_by!(name: bio_assoc,
project_id: @project_id)
ba = BiologicalAssociation.new(biological_relationship: br,
biological_association_object: otu,
biological_association_object_type: 'Otu',
biological_association_subject_type: 'CollectionObject')
retval[bio_assoc] = ba
end
}
end
retval
end
# @param [CSV::Row] row
# @return [Hash]
def make_ident(row)
ident = {}
cat_no = row['catalognumber'].split(' ')
unless cat_no.blank?
if @namespace.short_name != cat_no[0]
@errs.push("Namespace (#{cat_no[0]}) does not match import namespace (#{@namespace.short_name}).")
end
unless cat_no[1].blank?
id = Identifier::Local::CatalogNumber.find_or_initialize_by(namespace: @namespace,
project_id: @project_id,
identifier: cat_no[1])
ident[:id_cat_no] = id
end
end
occ_id = row['occurrenceid']
unless occ_id.blank?
id = Identifier::Global::OccurrenceId.find_or_initialize_by(relation: 'skos:exactMatch',
project_id: @project_id,
identifier: occ_id)
ident[:id_occ_id] = id
end
ident
end
# make_prsn: %w(georeferencedby),
# @param [CSV::Row] row
# @return [Hash]
def make_prsn(row)
ppl = {}
# check for person's name
name = row['georeferencedby']
unless name.blank?
if name.downcase.include?('verbatim')
else
# make a person to be used as a 'georeferencer'
parsed = Person.parser(name)
pr = Person.find_or_create_by!(last_name: parsed[0]['family'],
first_name: parsed[0]['given'])
ppl[:g_r] = pr
end
end
ppl
end
# rubocop:disable Metrics/MethodLength
# available data comes from Tulane geolocation action, reflected by the fact that the georefernce is a GeoLocate
# @param [CSV::Row] row
# @return [Georeference]
def make_gr(row)
geo_by = row['georeferencedby']
# lat, long = (lat.length > 0) ? lat : nil, (long.length > 0) ? long : nil
lat, long = row['decimallatitude'], row['decimallongitude']
if lat.nil? and long.nil?
uncert = nil
else
uncert = row['coordinateuncertaintyinmeters']
end
geo_by = '' if geo_by.nil?
if geo_by.downcase.include?('verbatim')
# make a verbatim reference
# fill in what we can, the real work is done when the collecting_event is added
g_r = Georeference::VerbatimData.new(error_radius: uncert)
else
# faking a Georeference::GeoLocate:
gl_req_params = {country: code_to_name(row['countrycode']),
state: row['stateprovince'],
county: row['county'],
Placename: row['municipality'],
Uncert: uncert,
Latitude: lat,
Longitude: long,
locality: row['locality'],
gc: geo_by}.stringify_keys
req = Georeference::GeoLocate::RequestUI.new(gl_req_params)
# 1) new the Georeference, without a collecting_event
g_r = Georeference::GeoLocate::GeoLocate.find_or_initialize_by(api_request: req.request_params_string,
project_id: @project_id)
# 2) save the information from the row in request_hash
if g_r.new_record?
g_r.api_request = req.request_params_string
# 3) build a fake iframe response in the form '52.65|-106.333333|3036|Unavailable'
text = "#{lat}|#{long}|#{uncert}|Unavailable"
# 4) use that fake to stimulate the parser to create the object
g_r.iframe_response = text
end
end
g_r
end
# @param [CSV::Row] row
# @return [Hash] of notes where key is object type
def make_notes(row)
ret_val = {}
begin
notes = {}
geo_remark = row['georeferenceremarks']
unless geo_remark.blank?
notes[:remark] = Note.new(text: geo_remark,
project_id: @project_id)
end
ret_val[:g_r] = notes unless notes.blank?
end
begin # collecting event notes
notes = {}
loc_remark = row['locationremarks']
unless loc_remark.blank?
notes[:remark] = Note.new(text: loc_remark,
note_object_attribute: :verbatim_locality,
project_id: @project_id)
end
ret_val[:c_e] = notes unless notes.blank?
end
begin # collection object notes
notes = {}
occ_remark = row['occurrenceremarks']
unless occ_remark.blank?
notes[:remark] = Note.new(text: occ_remark,
project_id: @project_id)
end
ret_val[:c_o] = notes unless notes.blank?
end
ret_val
end
#rubocop:enable Metrics/MethodLength
# @param [CSV::Row] row
# @return [Hash]
def make_tag(row)
ret_val = {}
ret_val.merge!(err: [])
ret_val.merge!(warn: [])
ret_val
end
#rubocop:disable Metrics/MethodLength
# a full set of symbolized filter names (kees, below) can be found in Utilities::Dates::REGEXP_DATES.keys
# @param [CSV::Row] row
# @return [Hash]
def make_ce(row)
ret_val = {}
kees = [:yyyy_mm_dd, :mm_dd_yy]
d_s = row['eventdate']
v_l = [row['municipality'], row['locality']].select {|name| name.present?}.join(':')
date_params = {}
unless d_s.blank?
trials = Utilities::Dates.hunt_dates(d_s, kees)
trials.each_key {|kee|
trial = trials[kee]
unless trial.blank?
case kee
when kees[0]
type = kee
when kees[1]
type = kee
end
sdd, sdm, sdy = trial[:start_date_day], trial[:start_date_month], trial[:start_date_year]
edd, edm, edy = trial[:end_date_day], trial[:end_date_month], trial[:end_date_year]
date_params[:start_date_day] = sdd unless sdd.blank?
date_params[:start_date_month] = sdm unless sdm.blank?
date_params[:start_date_year] = sdy unless sdy.blank?
date_params[:end_date_day] = edd unless edd.blank?
date_params[:end_date_month] = edm unless edm.blank?
date_params[:end_date_year] = edy unless edy.blank?
break # bail after the first with a date
end
}
end
g_a_list = [row['county'], row['stateprovince'], code_to_name(row['countrycode'])]
g_a_text = g_a_list.select {|name| name.present?}.join(':')
if g_a_text.blank?
g_a = nil
else
g_a_matches = GeographicArea.matching(g_a_text, true)
g_a = g_a_matches[g_a_text].try(:first)
end
hunt_params = {project_id: @project_id,
geographic_area: g_a,
verbatim_datum: row['geodeticdatum'],
verbatim_locality: v_l,
verbatim_date: d_s,
verbatim_label: row['locationremarks'],
verbatim_geolocation_uncertainty: row['coordinateuncertaintyinmeters'],
verbatim_latitude: row['decimallatitude'],
verbatim_longitude: row['decimallongitude'],
verbatim_collectors: row['recordedby']}.merge!(date_params)
c_e = CollectingEvent.find_or_initialize_by(hunt_params)
ret_val[:c_e] = c_e
ret_val.merge!(err: [])
ret_val.merge!(warn: [])
ret_val
end
#rubocop:enable Metrics/MethodLength
# @param [CSV::Row] row
# @return [Otu]
def make_otu(row)
Otu.new
end
#rubocop:disable Metrics/MethodLength
# make_co: %w(individualcount organismquantity organismquantitytype)
# http://rs.gbif.org/vocabulary/gbif/quantity_type_2015-07-10.xml
# @param [CSV::Row] row
# @return [Hash]
def make_co(row)
ret_val = {}
warn = []
err = []
ic = row['individualcount']
oq = row['organismquantity']
oqt = row['organismquantitytype']
combo = false
if ic.present? and (oqt.present? or oq.present?)
# warn.push('Choose either individualCount or the combination of organismQuantity and organismQuantityType,
# not both.')
combo = true
end
if (ic.to_i > 1) and combo
# leave ic alone
warn.push('individualCount has been used instead of the combination of organismQuantity and organismQuantityType.')
else
# set ic according to organismQuantityType
case oqt
when 'individuals'
ic = oq.to_i
when 'percentageOfSpecies',
'percentageOfBiovolume',
'percentageOfBiomass',
'percentageCoverage',
'dominScale',
'braunBlanquetScale',
'biomassAFDG',
'biomassG',
'biomassKg',
'biovolumeCubicMicrons',
'biovolumeMl'
ic = oq
else
warn.push("Unrecognized organismQuantityType #{oqt}.")
ic = oq
end
end
# ic will cause the selection of 'lot' or 'specimen'
c_o = Specimen.new(total: ic)
ret_val[:c_o] = c_o
ret_val.merge!(err: err)
ret_val.merge!(warn: warn)
ret_val
end
#rubocop:enable Metrics/MethodLength
#rubocop:disable Metrics/MethodLength
# make_tn: %w(scientificname taxonrank family kingdom)
# @param [CSV::Row] row
# @return [Hash]
def make_tn(row)
ret_val = {species: nil, genus: nil, tribe: nil}
this_kingdom = row['kingdom']
if @kingdom.try(:name) != this_kingdom
@kingdom = Protonym.find_or_create_by(name: this_kingdom,
rank_class: Ranks.lookup(:iczn, :kingdom),
project_id: @project_id)
if @kingdom.new_record?
@kingdom.parent = @root
@kingdom.save!
ret_val[:kingdom] = @kingdom
end
end
this_family = row['family']
if @family.try(:name) != this_family
@family = Protonym.find_or_create_by(name: this_family,
rank_class: Ranks.lookup(:iczn, :family),
project_id: @project_id)
if @family.new_record?
@family.parent = @kingdom
@family.save!
ret_val[:family] = @family
end
end
sn = row['scientificname']
snp = @parser.parse(sn)
# find or create Protonym based on exact match of row['scientificname'] and taxon_names.cached
# rubocop:disable Rails/SaveBang
t_n = Protonym.find_or_create_by(cached: snp[:scientificName][:canonical], project_id: @project_id)
this_rank = row['taxonrank'].downcase.to_sym
# rubocop:enable Rails/SaveBang
if t_n.new_record?
case this_rank
when :species
begin # find or create genus
genus_name = snp[:scientificName][:details][0][:genus][:string]
@genus = Protonym.find_or_create_by(name: genus_name,
parent: @family,
rank_class: Ranks.lookup(:iczn, :genus),
project_id: @project_id)
if @genus.new_record?
@genus.save!
ret_val[:new_genus] = @genus
end
end
species = snp[:scientificName][:details][0][:species]
t_n.parent = @genus
t_n.rank_class = Ranks.lookup(:iczn, :species)
t_n.name = species[:string]
# t_n.cached_author_year = snp[:scientificName][:details][0][:species][:authorship]
t_n.year_of_publication = species[:basionymAuthorTeam][:year].to_i
author_name = species[:basionymAuthorTeam][:authorTeam]
if species[:authorship].include?('(')
author_name = "(#{author_name})"
end
t_n.verbatim_author = author_name
ret_val[:species] = t_n
when :genus
genus = snp[:scientificName][:details][0][:uninomial]
t_n.parent = @family
t_n.rank_class = Ranks.lookup(:iczn, :genus)
t_n.name = genus[:string]
ret_val[:genus] = t_n
when :tribe
tribe = snp[:scientificName][:details][0][:uninomial]
t_n.parent = @family
t_n.rank_class = Ranks.lookup(:iczn, :tribe)
t_n.name = tribe[:string]
ret_val[:tribe] = t_n
else
raise "Unknown taxonRank #{this_rank}."
end
# t_n.create_otu
else
ret_val[this_rank] = t_n
end
ret_val
end
#rubocop:enable Metrics/MethodLength
# make_td: %w(scientificname basisofrecord individualcount organismquantity organismquantitytype recordedby)
# @param [CSV::Row] row
# @return [TaxonDetermination]
def make_td(row)
TaxonDetermination.new
end
# @param [String] code
# @return [nil, GeographicArea]
def code_to_name(code)
code.nil? ? nil : GeographicArea.where(iso_3166_a2: code).try(:first).try(:name)
end
=begin
2.3.3 :057 > headers
=> ["a", "b", "c", "d", "e", "f"]
2.3.3 :058 > mthds
=> {:foo=>["a", "b"], :bar=>["d", "e"], :blorf=>["f", "z"]}
2.3.3 :059 > mthds.select{|k,v| v & headers == v}
=> {:foo=>["a", "b"], :bar=>["d", "e"]}
2.3.3 :060 > mthds.select{|k,v| v & headers == v}.keys
=> [:foo, :bar]
2.3.3 :061 >
=end
# @param [Array] headers array of Strings which represent the TSV file headers
# @param [Hash] tasks hash of the method names (as keys) for the tasks, with lists of required headers (as values)
# @return [Array] of named tasks to perform, based on the presents of task's word list in the header list
# intersection of the word list from the tasks hash (per key) and the list of headers
def triage(headers, tasks)
tasks.select {|kee, vlu| (vlu & headers) == vlu}.keys
end
end
end