display for Flowcells

src/collection/pod5.rs

@@ -8,7 +8,7 @@ use rayon::prelude::*;
 use serde::{Deserialize, Serialize};
 use std::{
     collections::HashSet,
-    fmt::Display,
+    fmt::{self, Display},
     fs::{self, File, Metadata},
     hash::{Hash, Hasher},
     io::{BufReader, Read},
@@ -689,18 +689,31 @@ pub struct Pod5Run {
 
 #[derive(Debug, Serialize, Deserialize, Clone)]
 pub enum FlowCellExperiment {
-    WGSUnalignedMux(String),
-    WGSUnalignedDemux(String),
+    WGSPod5Mux(String),
+    WGSPod5Demux(String),
+}
+
+impl fmt::Display for FlowCellExperiment {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        write!(
+            f,
+            "{}",
+            match self {
+                FlowCellExperiment::WGSPod5Mux(_) => "WGS Pod5 Muxed",
+                FlowCellExperiment::WGSPod5Demux(_) => "WGS Pod5 Demuxed",
+            }
+        )
+    }
 }
 
 impl FlowCellExperiment {
     pub fn from_path(flowcell_path: &str) -> Option<Self> {
         for dir in list_directories(flowcell_path).ok().unwrap() {
             if dir == "pod5" {
-                return Some(FlowCellExperiment::WGSUnalignedMux(dir.to_string()));
+                return Some(FlowCellExperiment::WGSPod5Mux(dir.to_string()));
             }
             if &dir == "pod5_pass" {
-                return Some(FlowCellExperiment::WGSUnalignedDemux(dir.to_string()));
+                return Some(FlowCellExperiment::WGSPod5Demux(dir.to_string()));
             }
         }
         None
@@ -709,11 +722,11 @@ impl FlowCellExperiment {
     pub fn from_pod5_paths(all_paths: &Vec<String>) -> Option<Self> {
         for path in all_paths {
             if path.ends_with("/pod5/") || path.ends_with("/pod5") {
-                return Some(FlowCellExperiment::WGSUnalignedMux(path.to_string()));
+                return Some(FlowCellExperiment::WGSPod5Mux(path.to_string()));
             }
 
             if path.ends_with("/pod5_pass/") || path.ends_with("/pod5_pass") {
-                return Some(FlowCellExperiment::WGSUnalignedMux(path.to_string()));
+                return Some(FlowCellExperiment::WGSPod5Mux(path.to_string()));
             }
         }
         None
@@ -721,51 +734,51 @@ impl FlowCellExperiment {
 
     pub fn inner(&self) -> &str {
         match self {
-            FlowCellExperiment::WGSUnalignedMux(v) => v,
-            FlowCellExperiment::WGSUnalignedDemux(v) => v,
+            FlowCellExperiment::WGSPod5Mux(v) => v,
+            FlowCellExperiment::WGSPod5Demux(v) => v,
         }
     }
 }
 
-#[derive(Debug, Serialize, Deserialize, Clone)]
-pub struct FlowCellArchived {
-    pub archive_id: String,
-    pub last_seen: DateTime<Utc>,
-    pub run: MinKnowSampleSheet,
-}
-
-impl FlowCellArchived {
-    pub fn from_tar(tar_path: &str) -> Result<Vec<(String, u64, u64)>> {
-        // Open the tar file safely with context for errors
-        let file = File::open(tar_path)
-            .with_context(|| format!("Failed to open tar file at path: {}", tar_path))?;
-
-        let mut archive = tar::Archive::new(file);
-        let mut result = Vec::new();
-
-        // Iterate through the entries in the archive
-        for entry in archive.entries_with_seek()? {
-            let file = entry.context("Failed to read an entry from the tar archive")?;
-
-            // Extract file properties safely
-            let size = file.size();
-            let modified = file
-                .header()
-                .mtime()
-                .context("Failed to get modification time")?;
-            let path = file
-                .path()
-                .context("Failed to get file path from tar entry")?
-                .to_string_lossy()
-                .into_owned();
-
-            println!("{path}");
-            result.push((path, size, modified));
-        }
+// #[derive(Debug, Serialize, Deserialize, Clone)]
+// pub struct FlowCellArchived {
+//     pub archive_id: String,
+//     pub last_seen: DateTime<Utc>,
+//     pub run: MinKnowSampleSheet,
+// }
 
-        Ok(result)
-    }
-}
+// impl FlowCellArchived {
+//     pub fn from_tar(tar_path: &str) -> Result<Vec<(String, u64, u64)>> {
+//         // Open the tar file safely with context for errors
+//         let file = File::open(tar_path)
+//             .with_context(|| format!("Failed to open tar file at path: {}", tar_path))?;
+//
+//         let mut archive = tar::Archive::new(file);
+//         let mut result = Vec::new();
+//
+//         // Iterate through the entries in the archive
+//         for entry in archive.entries_with_seek()? {
+//             let file = entry.context("Failed to read an entry from the tar archive")?;
+//
+//             // Extract file properties safely
+//             let size = file.size();
+//             let modified = file
+//                 .header()
+//                 .mtime()
+//                 .context("Failed to get modification time")?;
+//             let path = file
+//                 .path()
+//                 .context("Failed to get file path from tar entry")?
+//                 .to_string_lossy()
+//                 .into_owned();
+//
+//             println!("{path}");
+//             result.push((path, size, modified));
+//         }
+//
+//         Ok(result)
+//     }
+// }
 
 pub fn scan_archive(
     tar_path: &str,
@@ -871,6 +884,19 @@ pub enum FlowCellLocation {
     Archived(String),
 }
 
+impl fmt::Display for FlowCellLocation {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        write!(
+            f,
+            "{}",
+            match self {
+                FlowCellLocation::Local(_) => "local",
+                FlowCellLocation::Archived(_) => "archived",
+            }
+        )
+    }
+}
+
 impl FlowCel {
     pub fn new(
         sample_sheet: MinKnowSampleSheet,
@@ -918,6 +944,7 @@ impl FlowCel {
         })
     }
 }
+
 #[derive(Debug, Serialize, Deserialize, Clone)]
 pub struct FlowCells {
     pub flow_cells: Vec<FlowCel>,
@@ -951,10 +978,14 @@ impl FlowCells {
 
         let inputs = IdsInput::load_json(inputs_path)?;
         flow_cells.iter_mut().for_each(|fc| {
-            fc.cases = inputs.data.iter().filter(|info| {
-                info.flow_cell == fc.run.sample_id
-                    && info.run == fc.run.experiment_id
-            }).cloned().collect();
+            fc.cases = inputs
+                .data
+                .iter()
+                .filter(|info| {
+                    info.flow_cell == fc.run.sample_id && info.run == fc.run.experiment_id
+                })
+                .cloned()
+                .collect();
         });
 
         Ok(Self { flow_cells })