cleaning up qc report for repo

Author: pnrobinson

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ga4ghphetools"
-version = "0.5.3"
+version = "0.5.4"
 edition = "2021"
 keywords = ["GA4GH", "Phenopacket Schema", "Human Phenotype Ontology"]
 description = "Generate GA4GH phenopackets from tabular data"

src/repo/gpt_repository.rs

@@ -16,7 +16,7 @@ pub struct GptRepository {
 
 
 impl GptRepository {
-    fn new(root_path: &str) -> Self {
+    pub fn new(root_path: &PathBuf) -> Self {
         let mut all_cohorts: Vec<CohortDir> = Vec::new();
         let entries = WalkDir::new(root_path)
             .min_depth(1)
@@ -77,12 +77,6 @@ mod tests {
     }
 
 
-    #[rstest]
-    fn test_repo(repo_path: String) {
-        let repo = GptRepository::new(&repo_path);
-        let repoqc = repo.repo_qc().unwrap();
-        
-    }
 
 
 

src/repo/mod.rs

@@ -3,11 +3,22 @@
 //! 
 //! 
 
+use std::path::PathBuf;
+
+use crate::repo::{gpt_repository::GptRepository, repo_qc::RepoQc};
+
 
 mod cohort_dir;
 mod cohort_qc;
 pub mod dashboard_data;
 mod disease_qc;
 mod gpt_repository;
 pub mod qc_report;
-mod repo_qc;
+pub mod repo_qc;
+
+
+
+pub fn get_repo_qc(path: &PathBuf) -> Result<RepoQc, String> {
+     let repo = GptRepository::new(path);
+     repo.repo_qc()
+}

src/repo/qc_report.rs

@@ -2,7 +2,8 @@ use std::collections::HashSet;
 
 
 
-#[derive(Debug, Clone, serde::Serialize)] // Serialize helps if passing to a web-based GUI
+#[derive(Debug, Clone, serde::Serialize)] 
+#[serde(rename_all = "camelCase")]
 pub struct QcReport {
     pub cohort_name: String,
     pub message: String,

src/repo/repo_qc.rs

@@ -4,7 +4,8 @@ use crate::repo::{cohort_qc::CohortQc, qc_report::QcReport};
 
 
 
-
+#[derive(Debug, Clone, serde::Serialize)] 
+#[serde(rename_all = "camelCase")]
 pub struct RepoQc {
     pub repo_path: String,
     pub cohort_count: usize,