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Commit ef9d884d authored by hh1966's avatar hh1966
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Refactor UDM export

parent 1f343b01
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lib/export/export_collections_udm_builder.rb
View file @ ef9d884d
......@@ -15,7 +15,7 @@ module Export
private
def build_xml(xml)
xml.UDM(DATABASE: '?', SEQUENCE: 0, TIMESTAMP: DateTime.now.to_s) {
xml.UDM(DATABASE: 'CHEMOTION', SEQUENCE: 1, TIMESTAMP: DateTime.now.to_s) {
xml.UDM_VERSION_PA(:MAJOR => 4, :MINOR => 0, :REVISION => 0, :BUILD => 1, :VERSIONTEXT => '4.0.0.1')
xml.CITATIONS {
@data.fetch('Literature', {}).each do |uuid, fields|
......@@ -112,14 +112,14 @@ module Export
# xml.METABOLITE_ID
# Identifier of a reactant in the reaction.
# @data.fetch('ReactionsReactantSample', {}).each do |product_uuid, _|
# xml.REACTANT_ID(:id => product_uuid)
# end
fetch_reaction_molecules('ReactionsReactantSample', uuid).each do |molecule_uuid, molecule_fields|
xml.REACTANT_ID molecule_uuid
end
# Identifier of a product in the reaction.
# @data.fetch('ReactionsProductSample', {}).each do |product_uuid, _|
# xml.PRODUCT_ID(:id => product_uuid)
# end
fetch_reaction_molecules('ReactionsProductSample', uuid).each do |molecule_uuid, molecule_fields|
xml.PRODUCT_ID molecule_uuid
end
# List of variations of a given reaction performed in different conditions.
xml.VARIATIONS {
......@@ -160,50 +160,24 @@ module Export
# xml.RESP_SCIENTIST
# xml.KEYWORDS
@data.fetch('ReactionsReactantSample', {}).each do |_uuid, _fields|
if _fields.fetch('reaction_id') == uuid
sample_uuid = _fields.fetch('sample_id')
sample_fields = @data.fetch('Sample', {}).fetch(sample_uuid)
build_reactants(xml, sample_uuid, sample_fields)
end
end
@data.fetch('ReactionsProductSample', {}).each do |_uuid, _fields|
if _fields.fetch('reaction_id') == uuid
sample_uuid = _fields.fetch('sample_id')
sample_fields = @data.fetch('Sample', {}).fetch(sample_uuid)
build_products(xml, sample_uuid, sample_fields)
end
fetch_reaction_molecules('ReactionsReactantSample', uuid).each do |molecule_uuid, molecule_fields|
build_reactants(xml, molecule_uuid, molecule_fields)
end
@data.fetch('ReactionsStartingMaterialSample', {}).each do |_uuid, _fields|
if _fields.fetch('reaction_id') == uuid
sample_uuid = _fields.fetch('sample_id')
sample_fields = @data.fetch('Sample', {}).fetch(sample_uuid)
build_reagents(xml, sample_uuid, sample_fields)
end
fetch_reaction_molecules('ReactionsProductSample', uuid).each do |molecule_uuid, molecule_fields|
build_products(xml, molecule_uuid, molecule_fields)
end
@data.fetch('?CATALYSTS?', {}).each do |_uuid, _fields|
if _fields.fetch('reaction_id') == uuid
sample_uuid = _fields.fetch('sample_id')
sample_fields = @data.fetch('Sample', {}).fetch(sample_uuid)
build_catalysts(xml, sample_uuid, sample_fields)
end
fetch_reaction_molecules('ReactionsStartingMaterialSample', uuid).each do |molecule_uuid, molecule_fields|
build_reagents(xml, molecule_uuid, molecule_fields)
end
@data.fetch('ReactionsSolventSample', {}).each do |_uuid, _fields|
if _fields.fetch('reaction_id') == uuid
sample_uuid = _fields.fetch('sample_id')
sample_fields = @data.fetch('Sample', {}).fetch(sample_uuid)
# fetch_reaction_molecules('?CATALYSTS?', uuid).each do |molecule_uuid, molecule_fields|
# build_catalysts(xml, sample_uuid, sample_fields)
# end
build_solvents(xml, sample_uuid, sample_fields)
end
fetch_reaction_molecules('ReactionsSolventSample', uuid).each do |molecule_uuid, molecule_fields|
build_solvents(xml, molecule_uuid, molecule_fields)
end
# build_conditions(xml, uuid, fields)
......@@ -247,7 +221,7 @@ module Export
def build_reactants(xml, uuid, fields)
xml.REACTANTS('ID' => uuid) {
xml.NAME fields.fetch('name')
xml.NAME fields.fetch('iupac_name')
# xml.AMOUNT
# xml.FORM
# xml.COLOR
......@@ -262,7 +236,7 @@ module Export
def build_products(xml, uuid, fields)
xml.PRODUCTS('ID' => uuid) {
xml.NAME fields.fetch('name')
xml.NAME fields.fetch('iupac_name')
# xml.AMOUNT
# xml.FORM
# xml.COLOR
......@@ -280,7 +254,7 @@ module Export
def build_reagents(xml, uuid, fields)
xml.REAGENTS('ID' => uuid) {
xml.NAME fields.fetch('name')
xml.NAME fields.fetch('iupac_name')
# xml.AMOUNT
# xml.FORM
# xml.COLOR
......@@ -295,7 +269,7 @@ module Export
def build_catalysts(xml, uuid, fields)
xml.CATALYSTS('ID' => uuid) {
xml.NAME fields.fetch('name')
xml.NAME fields.fetch('iupac_name')
# xml.AMOUNT
# xml.FORM
# xml.COLOR
......@@ -309,7 +283,7 @@ module Export
def build_solvents(xml, uuid, fields)
xml.SOLVENTS('ID' => uuid) {
xml.NAME fields.fetch('name')
xml.NAME fields.fetch('iupac_name')
# xml.AMOUNT
# xml.FORM
# xml.COLOR
......@@ -343,5 +317,36 @@ module Export
}
end
def fetch_reaction_samples(type, reaction_uuid)
# filter reaction_samples for the current reaction and type
reaction_samples = @data.fetch(type, {}).select do |uuid, fields|
fields.fetch('reaction_id') == reaction_uuid
end
# create an array of the sample uuids
uuids = reaction_samples.values.map do |reaction_sample|
reaction_sample.fetch('sample_id')
end
# filter samples according to sample uuids and return
return @data.fetch('Sample', {}).select do |uuid, _|
uuids.include? uuid
end
end
def fetch_reaction_molecules(type, reaction_uuid)
# get the samples for this reaction and type
samples = fetch_reaction_samples(type, reaction_uuid)
# create an array of the molecule uuids
uuids = samples.values.map do |sample|
sample.fetch('molecule_id')
end
# filter samples according to molecule uuids and return
return @data.fetch('Molecule', {}).select do |uuid, _|
uuids.include? uuid
end
end
end
end
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