Add plot samples

src/areas/models.rs

@@ -57,6 +57,13 @@ pub struct Area {
     geom: Option<Value>,
 }
 
+#[derive(ToSchema, Serialize)]
+pub struct AreaBasicWithProject {
+    pub id: Uuid,
+    pub name: Option<String>,
+    pub project: crate::common::models::GenericNameAndID,
+}
+
 // impl Sensor {
 //     pub fn from(sensor_db: crate::db::sensor::Model) -> Self {
 //         Sensor {

src/common/models.rs

@@ -1,9 +1,18 @@
+use sea_orm::FromQueryResult;
 use serde::Deserialize;
+use serde::Serialize;
 use utoipa::ToSchema;
+use uuid::Uuid;
 
 #[derive(ToSchema, Deserialize, Default)]
 pub struct FilterOptions {
     pub filter: Option<String>, // JSON-encoded filter
     pub range: Option<String>,  // range in the format "[0,24]"
     pub sort: Option<String>,   // sort in the format '["id", "ASC"]'
 }
+
+#[derive(ToSchema, Serialize, FromQueryResult)]
+pub struct GenericNameAndID {
+    pub id: Uuid,
+    pub name: String,
+}

src/main.rs

@@ -60,6 +60,7 @@ async fn main() {
         .nest("/v1/plots", plots::views::router(db.clone()))
         .nest("/v1/areas", areas::views::router(db.clone()))
         .nest("/v1/projects", projects::views::router(db.clone()))
+        .nest("/v1/plot_samples", samples::views::router(db.clone()))
         .merge(SwaggerUi::new("/swagger-ui").url("/api-docs/openapi.json", ApiDoc::openapi()))
         .merge(Redoc::with_url("/redoc", ApiDoc::openapi()))
         .merge(Scalar::with_url("/scalar", ApiDoc::openapi()));

src/plots/models.rs

@@ -18,6 +18,13 @@ pub struct PlotSimple {
     pub coord_y: Option<f64>,
     pub coord_z: Option<f64>,
 }
+#[derive(ToSchema, Serialize)]
+pub struct PlotBasicWithAreaAndProject {
+    pub id: Uuid,
+    pub name: String,
+    pub area: crate::areas::models::AreaBasicWithProject,
+}
+
 #[derive(ToSchema, Serialize)]
 pub struct Plot {
     id: Uuid,
@@ -78,6 +85,7 @@ impl From<areas::db::Model> for Area {
         }
     }
 }
+
 impl From<(PlotWithCoords, Option<Area>)> for Plot {
     fn from((plot_db, area_db_vec): (PlotWithCoords, Option<Area>)) -> Self {
         let area = area_db_vec.into_iter().next().map_or(

src/samples/mod.rs

@@ -1 +1,3 @@
 pub mod db;
+pub mod models;
+pub mod views;

src/samples/models.rs

@@ -0,0 +1,228 @@
+use sea_orm::ColumnTrait;
+use sea_orm::Condition;
+use sea_orm::EntityTrait;
+use sea_orm::{query::*, DatabaseConnection, QueryFilter, QueryOrder};
+use sea_query::Order;
+use serde::Serialize;
+use utoipa::ToSchema;
+use uuid::Uuid;
+
+#[derive(ToSchema, Serialize)]
+pub struct PlotSample {
+    pub id: Uuid,
+    pub name: String,
+    pub upper_depth_cm: f64,
+    pub lower_depth_cm: f64,
+    pub plot_id: Uuid,
+    pub sample_weight: Option<f64>,
+    pub subsample_weight: Option<f64>,
+    pub ph: Option<f64>,
+    pub rh: Option<f64>,
+    pub loi: Option<f64>,
+    pub mfc: Option<f64>,
+    pub c: Option<f64>,
+    pub n: Option<f64>,
+    pub cn: Option<f64>,
+    pub clay_percent: Option<f64>,
+    pub silt_percent: Option<f64>,
+    pub sand_percent: Option<f64>,
+    pub fe_ug_per_g: Option<f64>,
+    pub na_ug_per_g: Option<f64>,
+    pub al_ug_per_g: Option<f64>,
+    pub k_ug_per_g: Option<f64>,
+    pub ca_ug_per_g: Option<f64>,
+    pub mg_ug_per_g: Option<f64>,
+    pub mn_ug_per_g: Option<f64>,
+    pub s_ug_per_g: Option<f64>,
+    pub cl_ug_per_g: Option<f64>,
+    pub p_ug_per_g: Option<f64>,
+    pub si_ug_per_g: Option<f64>,
+    pub subsample_replica_weight: Option<f64>,
+    pub fungi_per_g: Option<f64>,
+    pub bacteria_per_g: Option<f64>,
+    pub archea_per_g: Option<f64>,
+    pub methanogens_per_g: Option<f64>,
+    pub methanotrophs_per_g: Option<f64>,
+    pub replicate: i32,
+    pub plot: crate::plots::models::PlotBasicWithAreaAndProject,
+}
+
+impl PlotSample {
+    pub async fn get_all(
+        db: &DatabaseConnection,
+        condition: Condition,
+        order_column: <super::db::Entity as sea_orm::EntityTrait>::Column,
+        order_direction: Order,
+        offset: u64,
+        limit: u64,
+    ) -> Vec<Self> {
+        let samples = crate::samples::db::Entity::find()
+            .filter(condition)
+            .order_by(order_column, order_direction)
+            .offset(offset)
+            .limit(limit)
+            .all(db)
+            .await
+            .unwrap();
+
+        let mut plot_samples: Vec<PlotSample> = Vec::new();
+
+        for sample in samples {
+            let plot_obj = crate::plots::db::Entity::find()
+                .filter(crate::plots::db::Column::Id.eq(sample.plot_id))
+                .one(db)
+                .await
+                .unwrap()
+                .unwrap();
+
+            let area = crate::areas::db::Entity::find()
+                .filter(crate::areas::db::Column::Id.eq(plot_obj.area_id))
+                .one(db)
+                .await
+                .unwrap()
+                .unwrap();
+
+            let project = crate::projects::db::Entity::find()
+                .filter(crate::projects::db::Column::Id.eq(area.project_id))
+                .one(db)
+                .await
+                .unwrap()
+                .unwrap();
+
+            let plot = crate::plots::models::PlotBasicWithAreaAndProject {
+                id: plot_obj.id,
+                name: plot_obj.name,
+                area: crate::areas::models::AreaBasicWithProject {
+                    id: area.id,
+                    name: area.name,
+                    project: crate::common::models::GenericNameAndID {
+                        id: project.id,
+                        name: project.name,
+                    },
+                },
+            };
+
+            plot_samples.push(PlotSample {
+                id: sample.id,
+                name: sample.name,
+                upper_depth_cm: sample.upper_depth_cm,
+                lower_depth_cm: sample.lower_depth_cm,
+                plot_id: sample.plot_id,
+                sample_weight: sample.sample_weight,
+                subsample_weight: sample.subsample_weight,
+                ph: sample.ph,
+                rh: sample.rh,
+                loi: sample.loi,
+                mfc: sample.mfc,
+                c: sample.c,
+                n: sample.n,
+                cn: sample.cn,
+                clay_percent: sample.clay_percent,
+                silt_percent: sample.silt_percent,
+                sand_percent: sample.sand_percent,
+                fe_ug_per_g: sample.fe_ug_per_g,
+                na_ug_per_g: sample.na_ug_per_g,
+                al_ug_per_g: sample.al_ug_per_g,
+                k_ug_per_g: sample.k_ug_per_g,
+                ca_ug_per_g: sample.ca_ug_per_g,
+                mg_ug_per_g: sample.mg_ug_per_g,
+                mn_ug_per_g: sample.mn_ug_per_g,
+                s_ug_per_g: sample.s_ug_per_g,
+                cl_ug_per_g: sample.cl_ug_per_g,
+                p_ug_per_g: sample.p_ug_per_g,
+                si_ug_per_g: sample.si_ug_per_g,
+                subsample_replica_weight: sample.subsample_replica_weight,
+                fungi_per_g: sample.fungi_per_g,
+                bacteria_per_g: sample.bacteria_per_g,
+                archea_per_g: sample.archea_per_g,
+                methanogens_per_g: sample.methanogens_per_g,
+                methanotrophs_per_g: sample.methanotrophs_per_g,
+                replicate: sample.replicate,
+                plot: plot,
+            });
+        }
+        plot_samples
+    }
+
+    pub async fn get_one(id: Uuid, db: &DatabaseConnection) -> Option<Self> {
+        let sample = crate::samples::db::Entity::find()
+            .filter(crate::samples::db::Column::Id.eq(id))
+            .one(db)
+            .await
+            .unwrap()
+            .unwrap();
+
+        let plot_obj = crate::plots::db::Entity::find()
+            .filter(crate::plots::db::Column::Id.eq(sample.plot_id))
+            .one(db)
+            .await
+            .unwrap()
+            .unwrap();
+
+        let area = crate::areas::db::Entity::find()
+            .filter(crate::areas::db::Column::Id.eq(plot_obj.area_id))
+            .one(db)
+            .await
+            .unwrap()
+            .unwrap();
+
+        let project = crate::projects::db::Entity::find()
+            .filter(crate::projects::db::Column::Id.eq(area.project_id))
+            .one(db)
+            .await
+            .unwrap()
+            .unwrap();
+
+        let plot = crate::plots::models::PlotBasicWithAreaAndProject {
+            id: plot_obj.id,
+            name: plot_obj.name,
+            area: crate::areas::models::AreaBasicWithProject {
+                id: area.id,
+                name: area.name,
+                project: crate::common::models::GenericNameAndID {
+                    id: project.id,
+                    name: project.name,
+                },
+            },
+        };
+
+        Some(PlotSample {
+            id: sample.id,
+            name: sample.name,
+            upper_depth_cm: sample.upper_depth_cm,
+            lower_depth_cm: sample.lower_depth_cm,
+            plot_id: sample.plot_id,
+            sample_weight: sample.sample_weight,
+            subsample_weight: sample.subsample_weight,
+            ph: sample.ph,
+            rh: sample.rh,
+            loi: sample.loi,
+            mfc: sample.mfc,
+            c: sample.c,
+            n: sample.n,
+            cn: sample.cn,
+            clay_percent: sample.clay_percent,
+            silt_percent: sample.silt_percent,
+            sand_percent: sample.sand_percent,
+            fe_ug_per_g: sample.fe_ug_per_g,
+            na_ug_per_g: sample.na_ug_per_g,
+            al_ug_per_g: sample.al_ug_per_g,
+            k_ug_per_g: sample.k_ug_per_g,
+            ca_ug_per_g: sample.ca_ug_per_g,
+            mg_ug_per_g: sample.mg_ug_per_g,
+            mn_ug_per_g: sample.mn_ug_per_g,
+            s_ug_per_g: sample.s_ug_per_g,
+            cl_ug_per_g: sample.cl_ug_per_g,
+            p_ug_per_g: sample.p_ug_per_g,
+            si_ug_per_g: sample.si_ug_per_g,
+            subsample_replica_weight: sample.subsample_replica_weight,
+            fungi_per_g: sample.fungi_per_g,
+            bacteria_per_g: sample.bacteria_per_g,
+            archea_per_g: sample.archea_per_g,
+            methanogens_per_g: sample.methanogens_per_g,
+            methanotrophs_per_g: sample.methanotrophs_per_g,
+            replicate: sample.replicate,
+            plot: plot,
+        })
+    }
+}