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implemented the 'exclude' term functionality
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@mdorf
mdorf committed Jan 7, 2022
1 parent 5db44d3 commit e288677
Showing 1 changed file with 71 additions and 39 deletions.
110 changes: 71 additions & 39 deletions bao_cedar_template_converter.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,9 @@
container: 'container' # same as whole branch, except the term itself should not be explicitly selected
}

UNKNOWN_ONTOLOGY = "Unknown Ontology"


def sanitize_input_for_json(str)
str.gsub("\"", "'").gsub(/[\r\n\t]/, " ")
end
Expand Down Expand Up @@ -121,7 +124,11 @@ def post_template_to_cedar(cedar_template_json, template_type)

def usable_value(val)
if val.key?("spec")
return [BAO_SPEC_FIELD_ENUM[:item], BAO_SPEC_FIELD_ENUM[:wholebranch], BAO_SPEC_FIELD_ENUM[:container]].include?(val["spec"])
return [BAO_SPEC_FIELD_ENUM[:item],
BAO_SPEC_FIELD_ENUM[:wholebranch],
BAO_SPEC_FIELD_ENUM[:container],
BAO_SPEC_FIELD_ENUM[:exclude]
].include?(val["spec"])
end
false
end
Expand All @@ -138,33 +145,52 @@ def create_cedar_controlled_value(orig_value, bp_ontologies, bp_terms)
bp_term = find_term_in_bioportal(orig_value["uri"])
bp_terms[orig_value["uri"]] = bp_term = not_found unless bp_term
end
cedar_value = {}
cedar_val = {
"uri" => orig_value["uri"]
}

if bp_term != not_found
ont_acronym = get_acronym_from_id(bp_term["links"]["ontology"])
cedar_value = {}
cedar_val = {
"uri" => orig_value["uri"],
"source" => "#{bp_ontologies[ont_acronym]} (#{ont_acronym})"
}

if [BAO_SPEC_FIELD_ENUM[:container], BAO_SPEC_FIELD_ENUM[:wholebranch]].include?(orig_value["spec"])
branch_val = cedar_val.dup.merge({
"acronym" => ont_acronym,
"name" => bp_term["prefLabel"],
"maxDepth" => 0
cedar_val["source"] = "#{bp_ontologies[ont_acronym]} (#{ont_acronym})"

if BAO_SPEC_FIELD_ENUM[:exclude] == orig_value["spec"]
cedar_val["termUri"] = cedar_val.delete("uri")
cedar_val["sourceUri"] = cedar_val["termUri"]
action_val = cedar_val.dup.merge({
"type" => "OntologyClass",
"action" => "delete"
})
cedar_value["branch"] = branch_val
end
cedar_value["action"] = action_val
else
if [BAO_SPEC_FIELD_ENUM[:container], BAO_SPEC_FIELD_ENUM[:wholebranch]].include?(orig_value["spec"])
branch_val = cedar_val.dup.merge({
"acronym" => ont_acronym,
"name" => bp_term["prefLabel"],
"maxDepth" => 0
})
cedar_value["branch"] = branch_val
end

if [BAO_SPEC_FIELD_ENUM[:item], BAO_SPEC_FIELD_ENUM[:wholebranch]].include?(orig_value["spec"])
class_val = cedar_val.dup.merge({
"prefLabel" => bp_term["prefLabel"],
"label" => bp_term["prefLabel"],
"type" => "OntologyClass"
})
cedar_value["class"] = class_val
if [BAO_SPEC_FIELD_ENUM[:item], BAO_SPEC_FIELD_ENUM[:wholebranch]].include?(orig_value["spec"])
class_val = cedar_val.dup.merge({
"prefLabel" => bp_term["prefLabel"],
"label" => bp_term["prefLabel"],
"type" => "OntologyClass"
})
cedar_value["class"] = class_val
end
end
elsif BAO_SPEC_FIELD_ENUM[:item] == orig_value["spec"]
class_val = cedar_val.dup.merge({
"source" => UNKNOWN_ONTOLOGY,
"prefLabel" => orig_value["name"],
"label" => orig_value["name"],
"type" => "OntologyClass"
})
cedar_value["class"] = class_val
end
cedar_value = false if cedar_value.empty?
end
cedar_value
end
Expand Down Expand Up @@ -222,17 +248,20 @@ def create_controlled_field(orig_field, bp_ontologies, bp_terms)
cedar_field["_valueConstraints"]["branches"] = []
branches = []
classes = []
actions = []

orig_field["values"].each do |original_val|
converted_val = create_cedar_controlled_value(original_val, bp_ontologies, bp_terms)

if converted_val
converted_val.each do |key, val|
case key
when "branch"
branches << val
when "class"
classes << val
when "branch"
branches << val
when "class"
classes << val
when "action"
actions << val
end
end
end
Expand All @@ -246,6 +275,7 @@ def create_controlled_field(orig_field, bp_ontologies, bp_terms)
vc = cedar_field["_valueConstraints"]
vc["branches"].concat(branches)
vc["classes"].concat(classes)
vc["actions"] = actions unless actions.empty?
enable_uri_value_for_field(cedar_field)
cedar_field
end
Expand Down Expand Up @@ -301,20 +331,22 @@ def create_cedar_field(orig_field, bp_ontologies, bp_terms)
cedar_field = nil

case bao_field_type
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:full]
cedar_field = create_controlled_field(orig_field, bp_ontologies, bp_terms)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:url]
cedar_field = create_uri_field(orig_field)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:string]
cedar_field = create_freetext_field(orig_field)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:number]
cedar_field = create_numeric_field(orig_field)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:integer]
cedar_field = create_integer_field(orig_field)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:date]
cedar_field = create_date_field(orig_field)
else
cedar_field = create_uri_field(orig_field)
# ignore suggestion and treat field as controlled if values are present
# per @alexclark, I think that's a bug in our template, there shouldn't
# be any values listed for the URL type. The easy solution is just to
# ignore it, and we should fix that on our end too.
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:full] || !orig_field["values"]&.empty?
cedar_field = create_controlled_field(orig_field, bp_ontologies, bp_terms)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:string]
cedar_field = create_freetext_field(orig_field)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:number]
cedar_field = create_numeric_field(orig_field)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:integer]
cedar_field = create_integer_field(orig_field)
when BAO_INTPUT_TYPE_SUGGESTIONS_ENUM[:date]
cedar_field = create_date_field(orig_field)
else
cedar_field = create_uri_field(orig_field)
end
cedar_field
end
Expand Down

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