Migrations needed for modifications on the new batches NIH table (#1997)

* Migrations needed for modifications on the new batches NIH table

* Lint fixes

* PR review suggestions

Author: leandroradusky

db/migrate/20231030102203_add_original_batch_id_to_samples.rb

@@ -1,5 +1,27 @@
 class AddOriginalBatchIdToSamples < ActiveRecord::Migration
   def change
     add_column :samples, :original_batch_id, :integer
+
+    Sample.preload(:batch).find_each do |sample|
+      if sample.batch
+        sample.original_batch_id = sample.batch.id
+        sample.save
+      elsif sample.box_id && sample.old_batch_number
+        institution_ids = TransferPackage
+          .select(:sender_institution_id)
+          .joins(:box_transfers)
+          .where(box_transfers: { box_id: sample.box_id })
+          .distinct
+      
+        original_batch = Batch.where(
+          institution_id: institution_ids,
+          batch_number: sample.old_batch_number
+        ).take
+        if original_batch
+          sample.original_batch_id = original_batch.id
+          sample.save
+        end
+      end
+    end
   end
 end

lib/tasks/batches_info.rake

@@ -0,0 +1,40 @@
+require 'csv'
+
+namespace :batches_info do
+  desc "Update batches information"
+  task :import, [:csv_file] => :environment do |task, args|
+    path = args[:csv_file] || abort("Usage: $> rake batches_info:import[path/to/file.csv] RAILS_ENV={env}")
+
+    CSV.foreach(path, headers: true) do |row|
+      batch = Batch.find_by(batch_number: row['virus_batch_number'])
+      if batch
+        batch.virus_shortname = row["virus_shortname"]
+        batch.target_organism_name = row["target_organism_name"]
+        batch.target_organism_taxonomy_id = row["target_organism_taxonomy_id"]
+        batch.isolate_name = row["isolate_name"]
+        batch.gisaid_id = row["gisaid_id"]
+        batch.nucleotide_db_id = row["nucleotide_db_id"]
+        batch.pango_lineage = row["pango_lineage"]
+        batch.who_label = row["who_label"]
+        batch.gisaid_clade = row["gisaid_clade"]
+        batch.virus_sample_source = row["virus_sample_source"]
+        batch.virus_sample_source_url = row["virus_sample_source_url"]
+        batch.virus_source = row["virus_source"]
+        batch.virus_location = row["virus_location"]
+        batch.virus_sample_type = row["virus_sample_type"]
+        batch.virus_sample_formulation = row["virus_sample_formulation"]
+        batch.virus_sample_concentration = row["virus_sample_concentration"]
+        batch.virus_sample_concentration_unit = row["virus_sample_concentration_unit"]
+        batch.reference_gene = row["virus_sample_concentration_reference_gene"]
+        batch.virus_sample_genome_equivalents = row["virus_sample_genome_equivalents"]
+        batch.virus_sample_genome_equivalents_unit = row["virus_sample_genome_equivalents_unit"]
+        batch.virus_sample_genome_equivalents_reference_gene = row["virus_sample_genome_equivalents_reference_gene"]
+        batch.virus_preinactivation_tcid50 = row["virus_preinactivation_tcid50"]
+        batch.virus_preinactivation_tcid50_unit = row["virus_preinactivation_tcid50_unit"]
+        batch.virus_sample_grow_cell_line = row["virus_sample_grow_cell_line"]
+
+        batch.save
+      end
+    end
+  end
+end