Pl/localization

tests/common/mod.rs

@@ -0,0 +1,28 @@
+pub use rulett::{
+    model::{Model, ModelDecl},
+    netgen::NetGenerator,
+    ob_tm::ObTm,
+    surface,
+    theory::{Signature, SignatureDecl},
+    ty::Ty,
+};
+
+pub use expect_test::expect;
+
+/// Merges multiple signatures.
+pub fn merge_signatures(sigs: &[Signature]) -> Signature {
+    let mut merged = Signature::new();
+    for sig in sigs {
+        for sort in sig.sorts() {
+            if !merged.sorts().any(|s| s == sort) {
+                merged.add_sort(sort).unwrap();
+            }
+        }
+        for (op, dom, cod) in sig.operations() {
+            if merged.interface(&op).is_none() {
+                merged.add_operation(op, dom.clone(), cod.clone()).unwrap();
+            }
+        }
+    }
+    merged
+}

tests/dependencies.rs

@@ -0,0 +1,292 @@
+//! Certain rules have implicit dependencies. For example, a phosphorylation
+//! rule can only fire if ATP is present, gene expression can only fire if
+//! transcription-translation machinery (RNA-polymerase, ribosomes, etc.)
+//! are present, etc.
+//!
+//! We call the totalty of dependencies an "environment". The required environment for the rule can be
+//! made explicit by putting it on either side of a rule. We can use product species in the signature to
+//! define environments as shown
+//! [here](https://q.uiver.app/#q=WzAsOCxbMSwwLCJUeU1vbGVjdWxlIl0sWzAsMSwiVHlBIl0sWzEsMSwiVHlCIl0sWzIsMSwiVHlDIl0sWzAsMiwiVHlBQiJdLFsxLDIsIlR5QUMiXSxbMiwyLCJUeUJDIl0sWzEsMywiVHlBQkMiXSxbMSwwXSxbMiwwXSxbMywwXSxbNCwxXSxbNSwxXSxbNCwyXSxbNiwyXSxbNSwzXSxbNiwzXSxbNyw0XSxbNyw1XSxbNyw2XV0=)
+//! or, using more suggestive labelling,
+//! [here](https://q.uiver.app/#q=WzAsOCxbMSwwLCJcXG1hdGhybXtUeU1vbGVjdWxlfSJdLFswLDEsIlxcbWF0aHJte1R5QX0iXSxbMSwxLCJcXG1hdGhybXtUeUJ9Il0sWzIsMSwiXFxtYXRocm17VHlDfSJdLFswLDIsIlxcbWF0aHJte0NlbGxYfSJdLFsxLDIsIlxcbWF0aHJte0NlbGxZfSJdLFsyLDIsIlxcbWF0aHJte0NlbGxafSJdLFsxLDMsIlxcbWF0aHJte0NlbGxPbW5pcG90ZW50fSJdLFsxLDBdLFsyLDBdLFszLDBdLFs0LDFdLFs1LDFdLFs0LDJdLFs2LDJdLFs1LDNdLFs2LDNdLFs3LDRdLFs3LDVdLFs3LDZdXQ==)
+//!
+//! I.e. an environment is a capability that combines the capabilities of its underlying species.
+//!
+//! Environments are "made available" in the same way as species: by providing
+//! "grounding signatures", that is, morphisms out of `[]`.
+//!
+//! Note: this requires product species (issue #9), which is currently not a priority.
+//! The example below illustrates the phoshporylation of CDC25, which requires either a
+//! CDK1.CCNB1 or CDK1.CCNB2 complex. We show that this reaction fires in a cell that expresses only
+//! - CDK1 and CCNB1
+//! - CDK1 and CCNB2
+//!
+//! but does not fire in a cell that expresses only
+//! - CCNB1 and CCNB2
+//!
+//! The signature can be illustrated as follows:
+//! https://q.uiver.app/#q=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
+//!
+//! Note that we do not model complex formation explicitly. The purpose for providing an environment is
+//! to allow modelers to optionally abstract away such detailed reactions.
+
+mod common;
+use common::*;
+
+/// Base signature.
+fn base_signature() -> Signature {
+    Signature::parse([
+        SignatureDecl::sort("TyMolecule"),
+        SignatureDecl::sort("TyCDK1"),
+        SignatureDecl::sort("TyCCNB1"),
+        SignatureDecl::sort("TyCCNB2"),
+        SignatureDecl::sort("Res"),
+        SignatureDecl::operation("iota_cdk1", [Ty::sort("TyCDK1")], Ty::sort("TyMolecule")),
+        SignatureDecl::operation("iota_ccnb1", [Ty::sort("TyCCNB1")], Ty::sort("TyMolecule")),
+        SignatureDecl::operation("iota_ccnb2", [Ty::sort("TyCCNB2")], Ty::sort("TyMolecule")),
+    ])
+    .unwrap()
+}
+
+/// Signature for the model environment.
+fn environment_signature() -> Signature {
+    Signature::parse([
+        // Define different cell lines in terms of their components (note that this has currently no effect, i.e. can be considered annotation).
+        SignatureDecl::sort("TyCDK1"),
+        SignatureDecl::sort("TyCCNB1"),
+        SignatureDecl::sort("TyCCNB2"),
+        SignatureDecl::sort("CellLine1"),
+        SignatureDecl::sort("CellLine2"),
+        SignatureDecl::sort("CellLine3"),
+        SignatureDecl::sort("CellOmnipotent"),
+        SignatureDecl::operation("iota_cl1_cdk1", [Ty::sort("CellLine1")], Ty::sort("TyCDK1")),
+        SignatureDecl::operation("iota_cl1_ccnb1", [Ty::sort("CellLine1")], Ty::sort("TyCCNB1")),
+        SignatureDecl::operation("iota_cl2_cdk1", [Ty::sort("CellLine2")], Ty::sort("TyCDK1")),
+        SignatureDecl::operation("iota_cl2_ccnb2", [Ty::sort("CellLine2")], Ty::sort("TyCCNB2")),
+        SignatureDecl::operation("iota_cl3_ccnb1", [Ty::sort("CellLine3")], Ty::sort("TyCCNB1")),
+        SignatureDecl::operation("iota_cl3_ccnb2", [Ty::sort("CellLine3")], Ty::sort("TyCCNB2")),
+        SignatureDecl::operation(
+            "iota_omni_1",
+            [Ty::sort("CellOmnipotent")],
+            Ty::sort("CellLine1"),
+        ),
+        SignatureDecl::operation(
+            "iota_omni_2",
+            [Ty::sort("CellOmnipotent")],
+            Ty::sort("CellLine2"),
+        ),
+        SignatureDecl::operation(
+            "iota_omni_3",
+            [Ty::sort("CellOmnipotent")],
+            Ty::sort("CellLine3"),
+        ),
+        // Define CellLine12 as coproduct of CellLine1 and CellLine2
+        SignatureDecl::sort("CellLine12"),
+        SignatureDecl::operation("iota_cl1in12", [Ty::sort("CellLine1")], Ty::sort("CellLine12")),
+        SignatureDecl::operation("iota_cl2in12", [Ty::sort("CellLine2")], Ty::sort("CellLine12")),
+        SignatureDecl::sort("TyEnv"),
+        SignatureDecl::operation("iota_cl12", [Ty::sort("CellLine12")], Ty::sort("TyEnv")),
+        SignatureDecl::operation("iota_cl3", [Ty::sort("CellLine3")], Ty::sort("TyEnv")),
+    ])
+    .unwrap()
+}
+
+/// Signature to ground the base in `[]``.
+fn ground_base() -> Signature {
+    Signature::parse([
+        SignatureDecl::sort("Res"),
+        SignatureDecl::operation("u", [], Ty::sort("Res")),
+        SignatureDecl::operation("p", [], Ty::sort("Res")),
+    ])
+    .unwrap()
+}
+
+/// Signature to ground the environment in `[]`.
+fn ground_environment(n: i32) -> Signature {
+    Signature::parse([
+        SignatureDecl::sort(format!("CellLine{n}")),
+        SignatureDecl::operation(format!("!env{n}"), [], Ty::sort(format!("CellLine{n}"))),
+    ])
+    .unwrap()
+}
+
+/// Full signature.
+fn signature(n: i32) -> Signature {
+    let sig1 = base_signature();
+    let sig2 = environment_signature();
+    let sig3 = ground_base();
+    let sig4 = ground_environment(n);
+    merge_signatures(&[sig1, sig2, sig3, sig4])
+}
+
+// Declares Model.
+fn model_decl() -> [ModelDecl; 3] {
+    use crate::surface::*;
+    [
+        ModelDecl::agent("CDC25", [ObTm::var("r")], [Ty::sort("Res")]),
+        ModelDecl::agent("Env", [ObTm::var("e")], [Ty::sort("TyEnv")]),
+        // TODO: perhaps we could add a field `dep` to rules for dependencies that occur on both lhs and rhs?
+        ModelDecl::rule(
+            "phosphorylation",
+            [ObTm::var("e")],
+            [Ty::sort("CellLine12")],
+            PatTm::tensor([
+                PatTm::res("Env", [MorTm::var("e")]),
+                PatTm::res("CDC25", [MorTm::app("u", [])]),
+            ]),
+            PatTm::tensor([
+                PatTm::res("Env", [MorTm::var("e")]),
+                PatTm::res("CDC25", [MorTm::app("p", [])]),
+            ]),
+        ),
+    ]
+}
+
+// Generates Model.
+fn model(n: i32) -> Model {
+    let decls = model_decl();
+    Model::parse(signature(n), decls).unwrap()
+}
+
+#[test]
+fn parse_signature() {
+    let expected = expect![[r#"
+        #/ sorts:
+        TyMolecule
+        TyCDK1
+        TyCCNB1
+        TyCCNB2
+        Res
+        CellLine1
+        CellLine2
+        CellLine3
+        CellOmnipotent
+        CellLine12
+        TyEnv
+        #/ operations:
+        iota_cdk1 : [TyCDK1] → TyMolecule
+        iota_ccnb1 : [TyCCNB1] → TyMolecule
+        iota_ccnb2 : [TyCCNB2] → TyMolecule
+        iota_cl1_cdk1 : [CellLine1] → TyCDK1
+        iota_cl1_ccnb1 : [CellLine1] → TyCCNB1
+        iota_cl2_cdk1 : [CellLine2] → TyCDK1
+        iota_cl2_ccnb2 : [CellLine2] → TyCCNB2
+        iota_cl3_ccnb1 : [CellLine3] → TyCCNB1
+        iota_cl3_ccnb2 : [CellLine3] → TyCCNB2
+        iota_omni_1 : [CellOmnipotent] → CellLine1
+        iota_omni_2 : [CellOmnipotent] → CellLine2
+        iota_omni_3 : [CellOmnipotent] → CellLine3
+        iota_cl1in12 : [CellLine1] → CellLine12
+        iota_cl2in12 : [CellLine2] → CellLine12
+        iota_cl12 : [CellLine12] → TyEnv
+        iota_cl3 : [CellLine3] → TyEnv
+        u : [] → Res
+        p : [] → Res
+        !env1 : [] → CellLine1
+    "#]];
+    expected.assert_eq(&signature(1).to_string());
+}
+
+#[test]
+fn parse_model() {
+    let expected = expect![[r#"
+        #/ sorts:
+        TyMolecule
+        TyCDK1
+        TyCCNB1
+        TyCCNB2
+        Res
+        CellLine1
+        CellLine2
+        CellLine3
+        CellOmnipotent
+        CellLine12
+        TyEnv
+        #/ operations:
+        iota_cdk1 : [TyCDK1] → TyMolecule
+        iota_ccnb1 : [TyCCNB1] → TyMolecule
+        iota_ccnb2 : [TyCCNB2] → TyMolecule
+        iota_cl1_cdk1 : [CellLine1] → TyCDK1
+        iota_cl1_ccnb1 : [CellLine1] → TyCCNB1
+        iota_cl2_cdk1 : [CellLine2] → TyCDK1
+        iota_cl2_ccnb2 : [CellLine2] → TyCCNB2
+        iota_cl3_ccnb1 : [CellLine3] → TyCCNB1
+        iota_cl3_ccnb2 : [CellLine3] → TyCCNB2
+        iota_omni_1 : [CellOmnipotent] → CellLine1
+        iota_omni_2 : [CellOmnipotent] → CellLine2
+        iota_omni_3 : [CellOmnipotent] → CellLine3
+        iota_cl1in12 : [CellLine1] → CellLine12
+        iota_cl2in12 : [CellLine2] → CellLine12
+        iota_cl12 : [CellLine12] → TyEnv
+        iota_cl3 : [CellLine3] → TyEnv
+        u : [] → Res
+        p : [] → Res
+        !env1 : [] → CellLine1
+        #/ agents:
+        [r] : [Res] ⊢ CDC25 [r]
+        [e] : [TyEnv] ⊢ Env [e]
+        #/ rules:
+        [e] : [CellLine12] ⊢
+          phosphorylation [e] : (Env [e], CDC25 [u []]) → (Env [e], CDC25 [p []])
+    "#]];
+    expected.assert_eq(&model(1).to_string());
+}
+
+// Test that reaction fires in CellLine1.
+#[test]
+fn generate_network_1() {
+    use itertools::Itertools;
+    let model = model(1);
+    let generator = NetGenerator::new(&model);
+
+    let species = expect![[r#"
+        CDC25 [u []]
+        CDC25 [p []]
+        Env [iota_cl12 [iota_cl1in12 [!env1 []]]]"#]];
+    species.assert_eq(&generator.species(2).join("\n"));
+
+    let transitions = expect![[r#"
+        phosphorylation [iota_cl1in12 [!env1 []]]
+          : (Env [iota_cl1in12 [!env1 []]], CDC25 [u []])
+          → (Env [iota_cl1in12 [!env1 []]], CDC25 [p []])"#]];
+    transitions.assert_eq(&generator.transitions(2).join("\n"));
+}
+
+// Test that reaction fires in CellLine2.
+#[test]
+fn generate_network_2() {
+    use itertools::Itertools;
+    let model = model(2);
+    let generator = NetGenerator::new(&model);
+
+    let species = expect![[r#"
+        CDC25 [u []]
+        CDC25 [p []]
+        Env [iota_cl12 [iota_cl2in12 [!env2 []]]]"#]];
+    species.assert_eq(&generator.species(2).join("\n"));
+
+    let transitions = expect![[r#"
+        phosphorylation [iota_cl2in12 [!env2 []]]
+          : (Env [iota_cl2in12 [!env2 []]], CDC25 [u []])
+          → (Env [iota_cl2in12 [!env2 []]], CDC25 [p []])"#]];
+    transitions.assert_eq(&generator.transitions(2).join("\n"));
+}
+
+// Test that reaction does not fire in CellLine3.
+#[test]
+fn generate_network_3() {
+    use itertools::Itertools;
+    let model = model(3);
+    let generator = NetGenerator::new(&model);
+
+    let species = expect![[r#"
+        CDC25 [u []]
+        CDC25 [p []]
+        Env [iota_cl3 [!env3 []]]"#]];
+    species.assert_eq(&generator.species(2).join("\n"));
+
+    let transitions = expect![""];
+    transitions.assert_eq(&generator.transitions(2).join("\n"));
+}
+
+// TODO: Create example for CellOmnipotent once we can handel product species (issue #9)