feat: adds library source material to sample

This is a squashed commit of the following commits from @grugna: * add Library Source Material - CDE 14808227 * adds PR link * typos * typos * typos * adding missing documentation * fmt format * resolve comments * Update swagger.yml * Update CHANGELOG.md * Update packages/ccdi-models/src/sample/metadata.rs * Update metadata.rs * remove value 'Other' * update to new CDE 15235975 Co-authored-by: e-t-k <[email protected]> Co-authored-by: claymcleod <[email protected]>
CBIIT · Nov 6, 2024 · 276b463 · 276b463
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,9 @@ Versioning](https://semver.org/spec/v2.0.0.html).
   their responses ([link to
   discussion](https://github.com/CBIIT/ccdi-federation-api/discussions/79),
   [#95](https://github.com/CBIIT/ccdi-federation-api/pull/95)).
+- Adds Library Source Material ([link to 
+  discussion](https://github.com/CBIIT/ccdi-federation-api/discussions/119),
+  [#118](https://github.com/CBIIT/ccdi-federation-api/pull/118))
 
 ### Revised
 

diff --git a/packages/ccdi-cde/src/v1/sample.rs b/packages/ccdi-cde/src/v1/sample.rs
@@ -2,11 +2,13 @@
 //! sample.
 
 mod disease_phase;
+mod library_source_material;
 mod library_strategy;
 mod tumor_classification;
 mod tumor_tissue_morphology;
 
 pub use disease_phase::DiseasePhase;
+pub use library_source_material::LibrarySourceMaterial;
 pub use library_strategy::LibraryStrategy;
 pub use tumor_classification::TumorClassification;
 pub use tumor_tissue_morphology::TumorTissueMorphology;
diff --git a/packages/ccdi-cde/src/v1/sample/library_source_material.rs b/packages/ccdi-cde/src/v1/sample/library_source_material.rs
@@ -0,0 +1,164 @@
+use introspect::Introspect;
+use rand::distributions::Standard;
+use rand::prelude::Distribution;
+use serde::Deserialize;
+use serde::Serialize;
+use utoipa::ToSchema;
+
+use crate::CDE;
+
+/// **`caDSR CDE 15235975 v1.00`**
+///
+/// This metadata element is defined by the caDSR as "TThe cell or cellular component that makes up the sample that has been prepared for testing or research purposes.".
+///
+/// Link:
+/// <https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15235975%20and%20ver_nr=1>
+#[derive(Clone, Debug, Deserialize, Eq, PartialEq, Serialize, ToSchema, Introspect)]
+#[schema(as = cde::v1::sample::LibrarySourceMaterial)]
+pub enum LibrarySourceMaterial {
+    /// `Bulk Cells`
+    ///
+    /// * **VM Long Name**: Bulk Cell Specimen
+    /// * **VM Public ID**: 7592130
+    /// * **Concept Code**: C178223
+    /// * **Begin Date**:   03/12/2024
+    ///
+    /// A biospecimen consisting of multiple cells intended to be analyzed as a pool.
+    #[serde(rename = "Bulk Cells")]
+    BulkCells,
+
+    /// `Bulk Nuclei`
+    ///
+    /// * **VM Long Name**: Bulk Nucleus Specimen
+    /// * **VM Public ID**: 7592129
+    /// * **Concept Code**: C178224
+    /// * **Begin Date**:   02/28/2024
+    ///
+    /// A biospecimen consisting of multiple nuclei intended to be analyzed as a pool.
+    #[serde(rename = "Bulk Nuclei")]
+    BulkNuclei,
+
+    /// `Bulk Tissue`
+    ///
+    /// * **VM Long Name**: Bulk Tissue Specimen
+    /// * **VM Public ID**: 7592128
+    /// * **Concept Code**: C178225
+    /// * **Begin Date**:   02/28/2024
+    ///
+    /// A biospecimen either derived from a whole tissue specimen or tissue section, which may consist of heterogeneous cells or tissues.
+    #[serde(rename = "Bulk Tissue")]
+    BulkTissue,
+
+    /// `Single-cells`
+    ///
+    /// * **VM Long Name**: Single Cell Suspension
+    /// * **VM Public ID**: 14838800
+    /// * **Concept Code**: C204464
+    /// * **Begin Date**:   03/12/2024
+    ///
+    /// A dilute suspension of cells intended to be further fractionated for assays focused on single-cells.
+    #[serde(rename = "Single-cells")]
+    SingleCells,
+
+    /// `Single-nuclei`
+    ///
+    /// * **VM Long Name**: Single Nucleus Suspension
+    /// * **VM Public ID**: 14838802
+    /// * **Concept Code**: C204465
+    /// * **Begin Date**:   03/12/2024
+    ///
+    /// A dilute suspension comprised of isolated intact cell nuclei intended to be further fractionated for assays focused on single-nuclei.
+    #[serde(rename = "Single-nuclei")]
+    SingleNuclei,
+
+    /// `Not Reported`
+    ///
+    /// * **VM Long Name**: Not Reported
+    /// * **VM Public ID**: 5612322
+    /// * **Concept Code**: C43234
+    /// * **Begin Date**:   03/01/2024
+    ///
+    /// Not provided or available.
+    #[serde(rename = "Not Reported")]
+    NotReported,
+}
+
+impl CDE for LibrarySourceMaterial {}
+
+impl std::fmt::Display for LibrarySourceMaterial {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        match self {
+            LibrarySourceMaterial::BulkCells => write!(f, "Bulk Cells"),
+            LibrarySourceMaterial::BulkNuclei => write!(f, "Bulk Nuclei"),
+            LibrarySourceMaterial::BulkTissue => write!(f, "Bulk Tissue"),
+            LibrarySourceMaterial::SingleCells => write!(f, "Single-cells"),
+            LibrarySourceMaterial::SingleNuclei => write!(f, "Single-nuclei"),
+            LibrarySourceMaterial::NotReported => write!(f, "Not Reported"),
+        }
+    }
+}
+
+impl Distribution<LibrarySourceMaterial> for Standard {
+    fn sample<R: rand::Rng + ?Sized>(&self, rng: &mut R) -> LibrarySourceMaterial {
+        match rng.gen_range(0..5) {
+            0 => LibrarySourceMaterial::BulkCells,
+            1 => LibrarySourceMaterial::BulkNuclei,
+            2 => LibrarySourceMaterial::BulkTissue,
+            3 => LibrarySourceMaterial::SingleCells,
+            4 => LibrarySourceMaterial::SingleNuclei,
+            _ => LibrarySourceMaterial::NotReported,
+        }
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn it_converts_to_string_correctly() {
+        assert_eq!(LibrarySourceMaterial::BulkCells.to_string(), "Bulk Cells");
+        assert_eq!(LibrarySourceMaterial::BulkNuclei.to_string(), "Bulk Nuclei");
+        assert_eq!(LibrarySourceMaterial::BulkTissue.to_string(), "Bulk Tissue");
+        assert_eq!(
+            LibrarySourceMaterial::SingleCells.to_string(),
+            "Single-cells"
+        );
+        assert_eq!(
+            LibrarySourceMaterial::SingleNuclei.to_string(),
+            "Single-nuclei"
+        );
+        assert_eq!(
+            LibrarySourceMaterial::NotReported.to_string(),
+            "Not Reported"
+        );
+    }
+
+    #[test]
+    fn it_serializes_to_json_correctly() {
+        assert_eq!(
+            serde_json::to_string(&LibrarySourceMaterial::BulkCells).unwrap(),
+            "\"Bulk Cells\""
+        );
+        assert_eq!(
+            serde_json::to_string(&LibrarySourceMaterial::BulkNuclei).unwrap(),
+            "\"Bulk Nuclei\""
+        );
+        assert_eq!(
+            serde_json::to_string(&LibrarySourceMaterial::BulkTissue).unwrap(),
+            "\"Bulk Tissue\""
+        );
+        assert_eq!(
+            serde_json::to_string(&LibrarySourceMaterial::SingleCells).unwrap(),
+            "\"Single-cells\""
+        );
+        assert_eq!(
+            serde_json::to_string(&LibrarySourceMaterial::SingleNuclei).unwrap(),
+            "\"Single-nuclei\""
+        );
+        assert_eq!(
+            serde_json::to_string(&LibrarySourceMaterial::NotReported).unwrap(),
+            "\"Not Reported\""
+        );
+    }
+}
diff --git a/packages/ccdi-models/src/metadata/field/description/harmonized/sample.rs b/packages/ccdi-models/src/metadata/field/description/harmonized/sample.rs
@@ -20,6 +20,7 @@ pub fn get_field_descriptions() -> Vec<description::Description> {
         crate::sample::metadata::Diagnosis::description(),
         cde::v1::sample::DiseasePhase::description(),
         cde::v1::sample::LibraryStrategy::description(),
+        cde::v1::sample::LibrarySourceMaterial::description(),
         cde::v2::sample::PreservationMethod::description(),
         cde::v2::sample::TissueType::description(),
         cde::v1::sample::TumorClassification::description(),
@@ -106,6 +107,28 @@ impl description::r#trait::Description for cde::v1::sample::LibraryStrategy {
     }
 }
 
+impl description::r#trait::Description for cde::v1::sample::LibrarySourceMaterial {
+    fn description() -> description::Description {
+        // SAFETY: these two unwraps are tested statically below in the test
+        // that constructs the description using `get_fields()`.
+        let entity = Self::entity().unwrap();
+        let members = Self::members().map(|member| member.unwrap());
+
+        description::Description::Harmonized(Harmonized::new(
+            Kind::Enum,
+            String::from("library_source_material"),
+            entity.description().to_string(),
+            "https://github.com/CBIIT/ccdi-federation-api/wiki/Sample-Metadata-Fields#library_source_material"
+                .parse::<Url>().unwrap(),
+            Some(Standard::new(
+                entity.standard_name().to_string(),
+                crate::Url::from(entity.standard_url().clone()),
+            )),
+            members,
+        ))
+    }
+}
+
 impl description::r#trait::Description for cde::v2::sample::PreservationMethod {
     fn description() -> description::Description {
         // SAFETY: these two unwraps are tested statically below in the test

diff --git a/packages/ccdi-models/src/metadata/field/unowned.rs b/packages/ccdi-models/src/metadata/field/unowned.rs
@@ -310,6 +310,15 @@ pub mod sample {
         ccdi_cde as cde
     );
 
+    unowned_field!(
+        LibrarySourceMaterial,
+        field::unowned::sample::LibrarySourceMaterial,
+        cde::v1::sample::LibrarySourceMaterial,
+        cde::v1::sample::LibrarySourceMaterial,
+        cde::v1::sample::LibrarySourceMaterial::NotReported,
+        ccdi_cde as cde
+    );
+
     unowned_field!(
         PreservationMethod,
         field::unowned::sample::PreservationMethod,

diff --git a/packages/ccdi-models/src/sample/metadata.rs b/packages/ccdi-models/src/sample/metadata.rs
@@ -56,10 +56,14 @@ pub struct Metadata {
     #[schema(value_type = field::unowned::sample::AgeAtCollection, nullable = true)]
     age_at_collection: Option<field::unowned::sample::AgeAtCollection>,
 
-    /// The strategy for constructing the sequencing library.
+    /// The library source material.
     #[schema(value_type = field::unowned::sample::LibraryStrategy, nullable = true)]
     library_strategy: Option<field::unowned::sample::LibraryStrategy>,
 
+    /// The strategy for constructing the sequencing library.
+    #[schema(value_type = field::unowned::sample::LibrarySourceMaterial, nullable = true)]
+    library_source_material: Option<field::unowned::sample::LibrarySourceMaterial>,
+
     /// The method used to maintain the sample or biospecimen in a viable state.
     #[schema(value_type = field::unowned::sample::PreservationMethod, nullable = true)]
     preservation_method: Option<field::unowned::sample::PreservationMethod>,
@@ -209,6 +213,42 @@ impl Metadata {
         self.library_strategy.as_ref()
     }
 
+    /// Gets the harmonized library source material for the [`Metadata`].
+    ///
+    /// # Examples
+    ///
+    /// ```
+    /// use ccdi_cde as cde;
+    /// use ccdi_models as models;
+    ///
+    /// use models::metadata::field::unowned::sample::LibrarySourceMaterial;
+    /// use models::sample::metadata::Builder;
+    ///
+    /// let metadata = Builder::default()
+    ///     .library_source_material(LibrarySourceMaterial::new(
+    ///         cde::v1::sample::LibrarySourceMaterial::BulkCells,
+    ///         None,
+    ///         None,
+    ///         None,
+    ///     ))
+    ///     .build();
+    ///
+    /// assert_eq!(
+    ///     metadata.library_source_material(),
+    ///     Some(&LibrarySourceMaterial::new(
+    ///         cde::v1::sample::LibrarySourceMaterial::BulkCells,
+    ///         None,
+    ///         None,
+    ///         None,
+    ///     ))
+    /// );
+    /// ```
+    pub fn library_source_material(
+        &self,
+    ) -> Option<&field::unowned::sample::LibrarySourceMaterial> {
+        self.library_source_material.as_ref()
+    }
+
     /// Gets the harmonized preservation method for the [`Metadata`].
     ///
     /// # Examples
@@ -565,6 +605,7 @@ impl Metadata {
             )),
             disease_phase: rand::random(),
             library_strategy: rand::random(),
+            library_source_material: rand::random(),
             preservation_method: rand::random(),
             tissue_type: rand::random(),
             tumor_classification: rand::random(),
@@ -624,7 +665,7 @@ mod tests {
         let metadata = builder::Builder::default().build();
         assert_eq!(
             &serde_json::to_string(&metadata).unwrap(),
-            "{\"age_at_diagnosis\":null,\"diagnosis\":null,\"disease_phase\":null,\"tissue_type\":null,\"tumor_classification\":null,\"tumor_tissue_morphology\":null,\"age_at_collection\":null,\"library_strategy\":null,\"preservation_method\":null,\"identifiers\":null,\"depositions\":null}"
+            "{\"age_at_diagnosis\":null,\"diagnosis\":null,\"disease_phase\":null,\"tissue_type\":null,\"tumor_classification\":null,\"tumor_tissue_morphology\":null,\"age_at_collection\":null,\"library_strategy\":null,\"library_source_material\":null,\"preservation_method\":null,\"identifiers\":null,\"depositions\":null}"
         );
     }
 }
diff --git a/packages/ccdi-models/src/sample/metadata/builder.rs b/packages/ccdi-models/src/sample/metadata/builder.rs
@@ -33,6 +33,9 @@ pub struct Builder {
     /// The strategy for constructing the sequencing library.
     library_strategy: Option<field::unowned::sample::LibraryStrategy>,
 
+    /// The library source material.
+    library_source_material: Option<field::unowned::sample::LibrarySourceMaterial>,
+
     /// The preservation method for this sample or biospecimen.
     preservation_method: Option<field::unowned::sample::PreservationMethod>,
 
@@ -231,6 +234,32 @@ impl Builder {
         self
     }
 
+    /// Sets the `library_source_material` field of the [`Builder`].
+    /// # Examples
+    ///
+    /// ```
+    /// use ccdi_cde as cde;
+    /// use ccdi_models as models;
+    ///
+    /// use models::metadata::field::unowned::sample::LibrarySourceMaterial;
+    /// use models::sample::metadata::Builder;
+    ///
+    /// let field = LibrarySourceMaterial::new(
+    ///     cde::v1::sample::LibrarySourceMaterial::BulkCells,
+    ///     None,
+    ///     None,
+    ///     None,
+    /// );
+    /// let builder = Builder::default().library_source_material(field);
+    /// ```
+    pub fn library_source_material(
+        mut self,
+        field: field::unowned::sample::LibrarySourceMaterial,
+    ) -> Self {
+        self.library_source_material = Some(field);
+        self
+    }
+
     /// Sets the `preservation_method` field of the [`Builder`].
     ///
     /// # Examples
@@ -408,6 +437,7 @@ impl Builder {
             diagnosis: self.diagnosis,
             disease_phase: self.disease_phase,
             library_strategy: self.library_strategy,
+            library_source_material: self.library_source_material,
             preservation_method: self.preservation_method,
             tissue_type: self.tissue_type,
             tumor_classification: self.tumor_classification,

diff --git a/packages/ccdi-openapi/src/api.rs b/packages/ccdi-openapi/src/api.rs
@@ -127,6 +127,7 @@ use utoipa::openapi;
         models::sample::metadata::Diagnosis,
         cde::v1::sample::DiseasePhase,
         cde::v1::sample::LibraryStrategy,
+        cde::v1::sample::LibrarySourceMaterial,
         cde::v2::sample::PreservationMethod,
         cde::v2::sample::TissueType,
         cde::v1::sample::TumorClassification,
@@ -168,6 +169,7 @@ use utoipa::openapi;
         field::unowned::sample::Diagnosis,
         field::unowned::sample::DiseasePhase,
         field::unowned::sample::LibraryStrategy,
+        field::unowned::sample::LibrarySourceMaterial,
         field::unowned::sample::PreservationMethod,
         field::unowned::sample::TissueType,
         field::unowned::sample::TumorClassification,