Merge pull request #11 from pcvolkmer/update_datamodel

chore: update data model

src/lib.rs

@@ -99,6 +99,7 @@ impl Mtb {
             prior_diagnostic_reports: None,
             systemic_therapies: None,
             metadata: None,
+            msi_findings: None,
         }
     }
 }

src/mtb.rs

@@ -39,6 +39,9 @@ pub struct Mtb {
     #[serde(skip_serializing_if = "Option::is_none")]
     pub metadata: Option<MvhMetadata>,
 
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub msi_findings: Option<Vec<Msi>>,
+
     #[serde(skip_serializing_if = "Option::is_none")]
     pub ngs_reports: Option<Vec<SomaticNgsReport>>,
 
@@ -1708,6 +1711,86 @@ pub enum MvhSubmissionType {
     Initial,
 }
 
+#[derive(Debug, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
+pub struct Msi {
+    pub id: String,
+
+    pub interpretation: MsiInterpretationCoding,
+
+    pub method: MsiMethodCoding,
+
+    pub patient: Reference,
+
+    pub specimen: Reference,
+
+    pub value: f64,
+}
+
+#[derive(Debug, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
+pub struct MsiInterpretationCoding {
+    pub code: MsiInterpretationCodingCode,
+
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub display: Option<String>,
+
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub system: Option<String>,
+
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub version: Option<String>,
+}
+
+#[derive(Debug, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
+#[serde(rename_all = "kebab-case")]
+pub enum MsiInterpretationCodingCode {
+    #[serde(rename = "mmr-deficient")]
+    MmrDeficient,
+
+    #[serde(rename = "mmr-proficient")]
+    MmrProficient,
+
+    #[serde(rename = "msi-high")]
+    MsiHigh,
+
+    #[serde(rename = "msi-low")]
+    MsiLow,
+
+    Stable,
+
+    Unknown,
+}
+
+#[derive(Debug, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
+pub struct MsiMethodCoding {
+    pub code: MsiMethodCodingCode,
+
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub display: Option<String>,
+
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub system: Option<String>,
+
+    #[serde(skip_serializing_if = "Option::is_none")]
+    pub version: Option<String>,
+}
+
+#[derive(Debug, Serialize, Deserialize)]
+#[serde(deny_unknown_fields)]
+pub enum MsiMethodCodingCode {
+    #[serde(rename = "bioinformatic")]
+    Bioinformatic,
+
+    #[serde(rename = "IHC")]
+    Ihc,
+
+    #[serde(rename = "PCR")]
+    Pcr,
+}
+
 #[derive(Debug, Serialize, Deserialize)]
 #[serde(deny_unknown_fields)]
 #[serde(rename_all = "camelCase")]