run sbatch

src/db/job/update.rs

+use std::process::Command;
 use log::info;
 use rusqlite::Connection;
 
 use crate::db::job::state::JobState;
+use crate::slurm::job::JobPath;
 use crate::slurm::job_request::JobRequest;
 
 impl JobRequest {
@@ -10,8 +12,11 @@ impl JobRequest {
         self.update(conn, state);
     }
 
-    pub fn submit(&self, conn: &Connection) {
+    pub fn submit(&self, conn: &Connection, job: JobPath) {
+        let job_id = self.run_sbatch(job);
+        info!("SLURM job id: {job_id}");
         let state = JobState::Submitted;
+        // todo: store SLURM job id in table too
         self.update(conn, state);
     }
 
@@ -26,4 +31,19 @@ impl JobRequest {
             &[(id.as_str())],
         ).expect("Update job status to {col}");
     }
+
+    fn run_sbatch(&self, job_path: JobPath) -> String {
+        let wd = job_path.path.parent().unwrap();
+        let output = Command::new("sbatch")
+            .arg("--parsable")
+            .arg("--output")
+            .arg(wd)
+            .arg("--error")
+            .arg(wd)
+            .arg(job_path.path)
+            .output()
+            .expect("sbatch");
+
+        String::from_utf8(output.stdout).expect("job id")
+    }
 }

src/main.rs

@@ -75,8 +75,7 @@ async fn main() {
             let job_path = job.create(&wd);
             if !args.dry_run {
                 job.stage(&conn);
-                // todo: sbatch this path
-                info!("{}", job_path.path.display())
+                job.submit(&conn, job_path);
             } else {
                 info!("--dry-run set, not submitting job to slurm");
             }

src/slurm/job.rs

@@ -2,6 +2,7 @@ use std::{fs, io};
 use std::fs::OpenOptions;
 use std::io::Write;
 use std::path::{Path, PathBuf};
+use std::process::Command;
 
 use chrono::Utc;
 use log::{info, warn};
@@ -11,7 +12,9 @@ use tinytemplate::TinyTemplate;
 use crate::slurm::job_request::{JobRequest, NxfParamsFile, PipelineParam, TargetGenome};
 use crate::WorkingDirectory;
 
-pub struct JobPath { pub path: PathBuf }
+pub struct JobPath {
+    pub path: PathBuf,
+}
 
 impl JobRequest {
     pub fn create(&self, wd: &WorkingDirectory) -> JobPath {