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Compare XML and database for tax id #748

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Compare XML and database for tax id #748

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e8d08db
Compare XML and database for tax id
maimux2x Oct 23, 2024
5695f93
fix indent
maimux2x Oct 23, 2024
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17 changes: 13 additions & 4 deletions api/app/models/database/bioproject/submitter.rb
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
class Database::BioProject::Submitter
class VisibilityMismatch < StandardError; end
class TaxIdMismatch < StandardError; end
class SubmissionIDOverflow < StandardError; end

PROJECT_DATA_TYPES = {
Expand Down Expand Up @@ -237,12 +238,20 @@ def submission_data_attrs(submission, doc)
},

doc.at("/PackageSet/Package/Project/Project/ProjectType/ProjectTypeSubmission/Target/Organism").then {
tax_id = _1&.[](:taxID) || begin
if organism_name = doc.at("/PackageSet/Package/Project/Project/ProjectType/ProjectTypeSubmission/Target/Organism/OrganismName")&.text
DRASearch::TaxName.where(search_name: organism_name, name_class: "scientific name").pick(:tax_id)
xml_tax_id = _1&.[](:taxID)

tax_id = if organism_name = doc.at("/PackageSet/Package/Project/Project/ProjectType/ProjectTypeSubmission/Target/Organism/OrganismName")&.text
drasearch_tax_id = DRASearch::TaxName.where(search_name: organism_name, name_class: "scientific name").pick(:tax_id)

if xml_tax_id
raise TaxIdMismatch if xml_tax_id != drasearch_tax_id.to_s

xml_tax_id
else
nil
drasearch_tax_id
end
else
nil
end

[ "target", "taxonomy_id", tax_id == "0" ? nil : tax_id, -1 ]
Expand Down
2 changes: 1 addition & 1 deletion api/spec/fixtures/files/bioproject/valid/full.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@
<ProjectType>
<ProjectTypeSubmission>
<Target sample_scope="project_type.sample_scope" material="project_type.material" capture="project_type.capture">
<Organism taxID="target.taxonomy_id || 0">
<Organism taxID="42">
<OrganismName>target.organism_name</OrganismName>
<Label>target.isolate_name_or_label?</Label>
<Strain>target.strain_breed_cultivar</Strain>
Expand Down
4 changes: 3 additions & 1 deletion api/spec/models/database/bioproject/submitter_spec.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,8 @@ def create_submission(visibility:, file:)
end

example "full" do
create :drasearch_tax_names, search_name: "target.organism_name", name_class: "scientific name", tax_id: 42

submission = create_submission(visibility: :private, file: "bioproject/valid/full.xml")

Database::BioProject::Submitter.new.submit submission
Expand Down Expand Up @@ -298,7 +300,7 @@ def create_submission(visibility:, file:)
{
form_name: "target",
data_name: "taxonomy_id",
data_value: "target.taxonomy_id || 0",
data_value: "42",
t_order: -1
},
{
Expand Down
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