Merge pull request #227 from OpenMined/madhava/resume

resume

Author: madhavajay

cli/src/cli/commands/run.rs

@@ -452,6 +452,9 @@ pub(crate) fn execute_with_logging(
     configure_child_process(&mut cmd);
 
     let mut child = cmd.spawn().context("Failed to execute Nextflow")?;
+    if let Ok(pid_path) = std::env::var("BIOVAULT_FLOW_PID_FILE") {
+        let _ = fs::write(pid_path, child.id().to_string());
+    }
 
     let log_path = std::env::var("BIOVAULT_DESKTOP_LOG_FILE").ok();
 

cli/src/cli/commands/run_dynamic.rs

@@ -192,6 +192,7 @@ fn should_force_x86_containers() -> bool {
 /// Returns None if Docker should auto-select (preferred for multi-arch images)
 /// Returns Some("linux/amd64") if x86 emulation is needed
 /// Returns Some("linux/arm64") only when explicitly required
+#[allow(dead_code)]
 fn get_container_platform(force_x86: bool) -> Option<&'static str> {
     if force_x86 || should_force_x86_containers() {
         return Some("linux/amd64");

cli/src/data/flows.rs

@@ -307,6 +307,14 @@ impl BioVaultDb {
         self.update_run_status(run_id, status, completed)
     }
 
+    pub fn update_flow_run_metadata(&self, run_id: i64, metadata: &str) -> Result<()> {
+        self.conn.execute(
+            "UPDATE flow_runs SET metadata = ?1 WHERE id = ?2",
+            params![metadata, run_id],
+        )?;
+        Ok(())
+    }
+
     /// Delete a run (flow or module)
     pub fn delete_run(&self, run_id: i64) -> Result<()> {
         self.conn

tests/scripts/devstack.sh

@@ -200,6 +200,28 @@ require_file() {
   [[ -f "$1" ]] || { echo "Missing required file: $1" >&2; exit 1; }
 }
 
+check_disk_space() {
+  local path="$1"
+  local threshold_kb=$((10 * 1024 * 1024)) # 10 GB in KB
+  local avail_kb=""
+  local resolved_path=""
+
+  if ! command -v df >/dev/null 2>&1; then
+    return 0
+  fi
+
+  avail_kb="$(df -Pk "$path" 2>/dev/null | awk 'NR==2 {print $4}')"
+  if [[ -z "$avail_kb" ]]; then
+    return 0
+  fi
+
+  if (( avail_kb < threshold_kb )); then
+    local avail_gb=$((avail_kb / 1024 / 1024))
+    resolved_path="$(abs_path "$path")"
+    echo "WARNING: Low disk space on ${resolved_path} (~${avail_gb}GB free). MinIO can stop working below ~10GB free." >&2
+  fi
+}
+
 is_windows() {
   case "$(uname -s)" in
     MINGW*|MSYS*|CYGWIN*) return 0 ;;
@@ -405,6 +427,7 @@ start_stack() {
   [[ -d "$SYFTBOX_DIR" ]] || { echo "Missing syftbox checkout at $SYFTBOX_DIR" >&2; exit 1; }
 
   mkdir -p "$SANDBOX_DIR"
+  check_disk_space "$SANDBOX_DIR"
 
   # Resolve client-mode first because it may force --skip-client-daemons (embedded mode).
   # This must happen before we build the sbdev argument list below.