adds id text fields for collections and specimens

Author: gsterjov

core/migrations/20251009001851_add_id_text_fields_to_collection_specimens.sql

@@ -0,0 +1,4 @@
+-- Modify "collection_events" table
+ALTER TABLE "public"."collection_events" ADD COLUMN "material_sample_id" character varying NULL;
+-- Modify "specimens" table
+ALTER TABLE "public"."specimens" ADD COLUMN "specimen_id" character varying NULL;

core/migrations/atlas.sum

@@ -1,4 +1,4 @@
-h1:ZrAjr6r13zRJ5SaMXxDC2u5U/vkPYNhc4Uot6Kdtnzw=
+h1:wCdAnjS63lgxAoaieRFUPRZdaPIYvgHR4sdWR/FBBLY=
 20250605060808_initial.sql h1:hN3eGaQNsqm+ws4akS+D+e+TqDUHZkZwPaFGW/Gyor4=
 20250605084357_drop_legacy_tables.sql h1:M0SD3ETeanSyo3GDWanw1xpGCJIQg7U11EE5IQ617EU=
 20250606063639_create_baseline_views.sql h1:bjh8zumpl5MFPRc1OAIB9jidVWxu1GPXAu5yGorDjFo=
@@ -26,3 +26,4 @@ h1:ZrAjr6r13zRJ5SaMXxDC2u5U/vkPYNhc4Uot6Kdtnzw=
 20251001124402_add_genbank_assembly_fields.sql h1:pp+8bnrzlheeCqyf8wo8FeTaxJM/CHJlNCmwBPdeqS0=
 20251003065225_create_data_products.sql h1:CYOkBdXXNn2CbN8z/TCmb8S6A8nYbnxFC6HnvIuLCfI=
 20251003065608_create_data_product_logs.sql h1:UGLIlEL4v+HZQos6hwaqgCj+kQcGgZMgDm7JHHJTTLc=
+20251009001851_add_id_text_fields_to_collection_specimens.sql h1:TbF1+MuV5z7cELp5pbpFIeAu9eP8XuiasodpebE+3YM=

core/schema.sql

@@ -372,7 +372,8 @@ CREATE TABLE organisms (
 CREATE TABLE specimens (
     entity_id varchar PRIMARY KEY NOT NULL,
     organism_id varchar REFERENCES organisms ON DELETE CASCADE NOT NULL,
-    name_id uuid REFERENCES names ON DELETE CASCADE NOT NULL
+    name_id uuid REFERENCES names ON DELETE CASCADE NOT NULL,
+    specimen_id varchar
 );
 
 
@@ -818,6 +819,7 @@ CREATE TABLE collection_events (
 
     name_id uuid REFERENCES names ON DELETE CASCADE NOT NULL,
     organism_id varchar REFERENCES organisms ON DELETE CASCADE NOT NULL,
+    material_sample_id varchar,
     field_collecting_id varchar,
 
     event_date date,

core/src/models/specimens.rs

@@ -13,6 +13,7 @@ pub struct Specimen {
     pub entity_id: String,
     pub organism_id: String,
     pub name_id: Uuid,
+    pub specimen_id: Option<String>,
 }
 
 
@@ -84,6 +85,7 @@ pub struct CollectionEvent {
     pub specimen_id: String,
     pub name_id: Uuid,
     pub organism_id: String,
+    pub material_sample_id: Option<String>,
     pub field_collecting_id: Option<String>,
 
     pub event_date: Option<chrono::NaiveDate>,

core/src/schema.rs

@@ -272,6 +272,7 @@ diesel::table! {
         environment_broad_scale -> Nullable<Varchar>,
         environment_local_scale -> Nullable<Varchar>,
         environment_medium -> Nullable<Varchar>,
+        material_sample_id -> Nullable<Varchar>,
     }
 }
 
@@ -847,6 +848,7 @@ diesel::table! {
         name_id -> Uuid,
         organism_id -> Varchar,
         entity_id -> Varchar,
+        specimen_id -> Nullable<Varchar>,
     }
 }
 

server/src/database/species.rs

@@ -51,6 +51,7 @@ pub struct MarkerSummary {
 pub struct SpecimenSummary {
     pub entity_id: String,
     pub organism_id: String,
+    pub specimen_id: Option<String>,
     pub collection_repository_id: Option<String>,
     pub collection_repository_code: Option<String>,
     pub institution_code: Option<String>,
@@ -206,6 +207,7 @@ impl SpeciesProvider {
             .select((
                 specimens::entity_id,
                 specimens::organism_id,
+                specimens::specimen_id,
                 accession_events::collection_repository_id.nullable(),
                 accession_events::collection_repository_code.nullable(),
                 accession_events::institution_code.nullable(),

server/src/http/graphql/common/specimens.rs

@@ -164,6 +164,7 @@ pub struct CollectionEvent {
     pub entity_id: String,
     pub specimen_id: String,
     pub organism_id: String,
+    pub material_sample_id: Option<String>,
     pub field_collecting_id: Option<String>,
 
     pub event_date: Option<chrono::NaiveDate>,
@@ -209,6 +210,7 @@ impl From<models::CollectionEvent> for CollectionEvent {
             entity_id: value.entity_id,
             specimen_id: value.specimen_id,
             organism_id: value.organism_id,
+            material_sample_id: value.material_sample_id,
             field_collecting_id: value.field_collecting_id,
             event_date: value.event_date,
             event_time: value.event_time,

server/src/http/graphql/species.rs

@@ -588,6 +588,7 @@ impl From<models::GenomicComponent> for GenomicComponent {
 pub struct SpecimenSummary {
     pub entity_id: String,
     pub organism_id: String,
+    pub specimen_id: Option<String>,
     pub collection_repository_id: Option<String>,
     pub collection_repository_code: Option<String>,
     pub institution_code: Option<String>,
@@ -614,6 +615,7 @@ impl From<species::SpecimenSummary> for SpecimenSummary {
         Self {
             entity_id: value.entity_id,
             organism_id: value.organism_id,
+            specimen_id: value.specimen_id,
             collection_repository_id: value.collection_repository_id,
             collection_repository_code: value.collection_repository_code,
             institution_code: value.institution_code,