add ebi fields to study

db/migrate/20250110153629_add_ebi_fields_to_study.rb

@@ -0,0 +1,7 @@
+class AddEbiFieldsToStudy < ActiveRecord::Migration[7.0]
+  def change
+    add_column :study, :ebi_library_strategy, :string, default: nil
+    add_column :study, :ebi_library_source, :string, default: nil
+    add_column :study, :ebi_library_selection, :string, default: nil
+  end
+end

db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema[7.0].define(version: 2024_12_11_144506) do
+ActiveRecord::Schema[7.0].define(version: 2025_01_10_153629) do
   create_table "aliquot", charset: "utf8mb3", collation: "utf8mb3_unicode_ci", force: :cascade do |t|
     t.string "id_lims", null: false, comment: "The LIMS system that the aliquot was created in"
     t.string "aliquot_uuid", null: false, comment: "The UUID of the aliquot in the LIMS system"
@@ -465,6 +465,9 @@
     t.string "data_deletion_period"
     t.string "contaminated_human_data_access_group"
     t.string "programme"
+    t.string "ebi_library_strategy"
+    t.string "ebi_library_source"
+    t.string "ebi_library_selection"
     t.index ["accession_number"], name: "study_accession_number_index"
     t.index ["id_lims", "id_study_lims"], name: "study_id_lims_id_study_lims_index", unique: true
     t.index ["id_study_lims"], name: "index_study_on_id_study_lims"
@@ -482,17 +485,6 @@
     t.index ["id_study_tmp"], name: "study_users_study_fk"
   end
 
-  add_foreign_key "bmap_flowcell", "sample", column: "id_sample_tmp", primary_key: "id_sample_tmp", name: "fk_bmap_flowcell_to_sample"
-  add_foreign_key "bmap_flowcell", "study", column: "id_study_tmp", primary_key: "id_study_tmp", name: "fk_bmap_flowcell_to_study"
-  add_foreign_key "flgen_plate", "sample", column: "id_sample_tmp", primary_key: "id_sample_tmp", name: "flgen_plate_sample_fk"
-  add_foreign_key "flgen_plate", "study", column: "id_study_tmp", primary_key: "id_study_tmp", name: "flgen_plate_study_fk"
-  add_foreign_key "iseq_flowcell", "sample", column: "id_sample_tmp", primary_key: "id_sample_tmp", name: "iseq_flowcell_sample_fk"
-  add_foreign_key "iseq_flowcell", "study", column: "id_study_tmp", primary_key: "id_study_tmp", name: "iseq_flowcell_study_fk"
-  add_foreign_key "oseq_flowcell", "sample", column: "id_sample_tmp", primary_key: "id_sample_tmp", name: "fk_oseq_flowcell_to_sample"
-  add_foreign_key "oseq_flowcell", "study", column: "id_study_tmp", primary_key: "id_study_tmp", name: "fk_oseq_flowcell_to_study"
-  add_foreign_key "pac_bio_run", "sample", column: "id_sample_tmp", primary_key: "id_sample_tmp", name: "fk_pac_bio_run_to_sample"
-  add_foreign_key "pac_bio_run", "study", column: "id_study_tmp", primary_key: "id_study_tmp", name: "fk_pac_bio_run_to_study"
-  add_foreign_key "qc_result", "sample", column: "id_sample_tmp", primary_key: "id_sample_tmp", name: "fk_qc_result_to_sample"
   add_foreign_key "samples_extraction_activity", "sample", column: "id_sample_tmp", primary_key: "id_sample_tmp"
   add_foreign_key "stock_resource", "sample", column: "id_sample_tmp", primary_key: "id_sample_tmp", name: "fk_stock_resource_to_sample"
   add_foreign_key "stock_resource", "study", column: "id_study_tmp", primary_key: "id_study_tmp", name: "fk_stock_resource_to_study"

db/views_schema.rb

@@ -1,32 +1 @@
-mlwh_wh_db = Rails.configuration.view_schema_mlwh_db
-event_wh_db = Rails.configuration.view_schema_ewh_db
-
-ViewsSchema.update_view(
-    'cherrypicked_samples',
-    <<~SQL.squish
-    SELECT mlwh_sample.description AS 'root_sample_id', mlwh_stock_resource.labware_human_barcode AS 'plate_barcode',
-    mlwh_sample.phenotype AS 'phenotype', mlwh_stock_resource.labware_coordinate AS 'coordinate',
-    mlwh_sample.created AS 'created', 'Tecan' as 'robot_type'
-    FROM #{mlwh_wh_db}.`sample` AS mlwh_sample
-    JOIN #{mlwh_wh_db}.stock_resource AS mlwh_stock_resource ON (mlwh_sample.id_sample_tmp = mlwh_stock_resource.id_sample_tmp)
-    JOIN #{event_wh_db}.subjects mlwh_events_subjects ON (mlwh_events_subjects.friendly_name = mlwh_sample.sanger_sample_id)
-    JOIN #{event_wh_db}.roles mlwh_events_roles ON (mlwh_events_roles.subject_id = mlwh_events_subjects.id)
-    JOIN #{event_wh_db}.events mlwh_events_events ON (mlwh_events_roles.event_id = mlwh_events_events.id)
-    JOIN #{event_wh_db}.event_types mlwh_events_event_types ON (mlwh_events_events.event_type_id = mlwh_events_event_types.id)
-    WHERE mlwh_events_event_types.key = 'cherrypick_layout_set'
-    UNION
-    SELECT mlwh_sample.description AS 'root_sample_id', mlwh_lh_sample.plate_barcode AS 'plate_barcode',
-    mlwh_sample.phenotype AS 'phenotype', mlwh_lh_sample.coordinate AS 'coordinate', mlwh_sample.created AS 'created',
-    IF(mlwh_events_event_types.key="lh_beckman_cp_destination_created","Beckman","Biosero") AS 'robot_type'
-    FROM #{mlwh_wh_db}.sample as mlwh_sample
-    JOIN #{mlwh_wh_db}.lighthouse_sample AS mlwh_lh_sample ON (mlwh_sample.uuid_sample_lims = mlwh_lh_sample.lh_sample_uuid)
-    JOIN #{event_wh_db}.subjects AS mlwh_events_subjects ON (mlwh_events_subjects.uuid = UNHEX(REPLACE(mlwh_lh_sample.lh_sample_uuid, '-', '')))
-    JOIN #{event_wh_db}.roles AS mlwh_events_roles ON (mlwh_events_roles.subject_id = mlwh_events_subjects.id)
-    JOIN #{event_wh_db}.events AS mlwh_events_events ON (mlwh_events_events.id = mlwh_events_roles.event_id)
-    JOIN #{event_wh_db}.event_types AS mlwh_events_event_types ON (mlwh_events_event_types.id = mlwh_events_events.event_type_id)
-    WHERE mlwh_events_event_types.key IN (
-      'lh_beckman_cp_destination_created', 'lh_biosero_cp_destination_plate_completed', 'lh_biosero_cp_destination_plate_partial_completed',
-      'lh_biosero_cp_error_recovered_destination_plate_completed','lh_biosero_cp_error_recovered_destination_plate_partial_completed'
-    )
-SQL
-)
+# This is an automatically generated file by rake:db:views:dump_schema