LB media and competent cells

crates/lab-adapters/src/backend/mod.rs

@@ -13,6 +13,7 @@ pub mod opentrons;
 mod procedure;
 mod profile;
 mod resources;
+pub mod run_sheet;
 mod typst;
 
 pub use adapters::{

crates/lab-adapters/src/backend/run_sheet.rs

@@ -0,0 +1,105 @@
+//! The operator run sheet for a reviewed plan's manual steps.
+//!
+//! A step an instrument runs arrives with its own operator document, rendered
+//! by the adapter that lowered it. A manual-control step has no adapter, so
+//! this is where its instructions land: one document for the whole plan, each
+//! step stating the operation it performs, the asset it uses, and the
+//! parameters it runs at.
+
+use crate::backend::document::{Block, Column, Doc, DocMeta, code, text};
+use crate::backend::typst;
+
+/// Everything a manual run sheet says.
+pub struct RunSheet {
+    /// The package whose entry workflow the plan runs.
+    pub package: String,
+    pub version: String,
+    /// The facility the plan allocated against, as display text.
+    pub facility: String,
+    /// The manual steps, in the order the plan performs them.
+    pub steps: Vec<RunStep>,
+}
+
+/// One manual step of the plan.
+pub struct RunStep {
+    /// What the operator does, e.g. "Centrifuge".
+    pub title: String,
+    /// The exact Procedure operation the step performs.
+    pub operation: String,
+    /// The asset the step uses, as display text.
+    pub asset: String,
+    /// Display-ready parameter names and values.
+    pub parameters: Vec<(String, String)>,
+}
+
+/// The style sheet a rendered run sheet imports, written beside the source as
+/// [`RUN_SHEET_STYLE_PATH`] so the directory typesets standalone.
+pub const RUN_SHEET_STYLE: &str = typst::STYLE;
+
+/// The file name the style sheet is written under.
+pub const RUN_SHEET_STYLE_PATH: &str = typst::STYLE_PATH;
+
+/// Render the run sheet as Typst source.
+pub fn render_run_sheet(sheet: &RunSheet) -> String {
+    let mut doc = Doc::new(DocMeta::new(
+        "Manual protocol",
+        format!("Operator run sheet for {} {}", sheet.package, sheet.version),
+        "",
+        sheet.facility.clone(),
+    ));
+    doc.notice([text(
+        "Generated from the reviewed facility plan. Perform each step in order and \
+         confirm it in the run ledger.",
+    )]);
+    for (index, step) in sheet.steps.iter().enumerate() {
+        doc.blocks.push(Block::Heading {
+            level: 1,
+            label: Some(format!("Step {}", index + 1)),
+            text: vec![text(step.title.clone())],
+        });
+        doc.para([
+            text("Perform "),
+            code(step.operation.clone()),
+            text(" using "),
+            code(step.asset.clone()),
+            text("."),
+        ]);
+        doc.table(
+            [Column::left("Parameter"), Column::left("Value")],
+            step.parameters
+                .iter()
+                .map(|(name, value)| vec![vec![code(name.clone())], vec![text(value.clone())]]),
+        );
+    }
+    typst::render(&doc)
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn renders_each_step_with_its_parameters() {
+        let source = render_run_sheet(&RunSheet {
+            package: "gll".to_owned(),
+            version: "0.1.0".to_owned(),
+            facility: "Genetic Logic Lab".to_owned(),
+            steps: vec![RunStep {
+                title: "Centrifuge".to_owned(),
+                operation: "https://www.lab-compiler.org/ns/procedure#Centrifuge".to_owned(),
+                asset: "bench_workstation".to_owned(),
+                parameters: vec![("force".to_owned(), "4000 rcf".to_owned())],
+            }],
+        });
+        assert!(
+            source.contains("Operator run sheet for gll 0.1.0"),
+            "{source}"
+        );
+        assert!(source.contains("Step 1"), "{source}");
+        assert!(source.contains("4000 rcf"), "{source}");
+        assert!(
+            source.contains("#import \"lab-style.typ\""),
+            "the sheet typesets against the bundled style: {source}"
+        );
+    }
+}

crates/lab-adapters/src/lib.rs

@@ -18,7 +18,7 @@ pub use backend::{
     ValidatedAdapterProfile, adapter_catalog, default_adapter_profile,
     lower_adapter_invocation_with_adapter, validate_adapter_profile,
 };
-pub use backend::{hamilton, inheco, opentrons};
+pub use backend::{hamilton, inheco, opentrons, run_sheet};
 pub use invocation::{
     ADAPTER_INVOCATIONS_SCHEMA_VERSION, AdapterInvocation, AdapterInvocationError,
     AdapterInvocationPlan, AdapterInvocationValidationError, adapter_invocation_id,