add workflow-monitor-path parameter

ebi-gdp · Sep 18, 2023 · 0fc7f10 · 0fc7f10
1 parent 84ff216
commit 0fc7f10
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Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/data/templates/callback.txt b/data/templates/callback.txt
@@ -8,7 +8,7 @@ set -euxo pipefail
 module load python-data/3.10-23.07
 
 # run the monitor in the background
-python3 {workflow_monitor_path} \
+{workflow_monitor_path} \
   --callback_token $CALLBACK_TOKEN \
   --namespace {namespace} &
 

diff --git a/src/main.rs b/src/main.rs
@@ -53,7 +53,10 @@ struct Args {
     globus_jar_path: PathBuf,
     /// Which platform namespace do you want to deploy to? [dev, test, prod]
     #[arg(short, long, value_enum)]
-    namespace: PlatformNamespace
+    namespace: PlatformNamespace,
+    /// Path to the workflow monitor binary (installed in a venv)
+    #[arg(long)]
+    workflow_monitor_path: PathBuf,
 }
 
 /// A directory for storing working data
@@ -105,7 +108,7 @@ async fn main() {
 
     if let Some(jobs) = jobs {
         for job in jobs {
-            let job_path = job.create(&wd, &args.globus_jar_path, &args.namespace);
+            let job_path = job.create(&wd, &args.globus_jar_path, &args.namespace, &args.workflow_monitor_path);
             if !args.dry_run {
                 job.stage(&conn);
                 job.submit(&conn, job_path);

diff --git a/src/slurm/job.rs b/src/slurm/job.rs
@@ -24,7 +24,8 @@ pub struct JobPath {
 }
 
 impl JobRequest {
-    pub fn create(&self, wd: &WorkingDirectory, globus_path: &PathBuf, namespace: &PlatformNamespace) -> JobPath {
+    pub fn create(&self, wd: &WorkingDirectory, globus_path: &PathBuf, namespace: &PlatformNamespace,
+    monitor_path: &PathBuf) -> JobPath {
         let instance_wd = WorkingDirectory { path: wd.path.join(&&self.pipeline_param.id) };
         info!("Creating job {} in working directory {}", &&self.pipeline_param.id, &instance_wd.path.display());
 
@@ -35,7 +36,7 @@ impl JobRequest {
         fs::create_dir(&instance_wd.path).expect("Create working directory");
 
         let header: Header = render_header(&&self.pipeline_param);
-        let callback: Callback = render_callback(&&self.pipeline_param, &namespace);
+        let callback: Callback = render_callback(&&self.pipeline_param, &namespace, &monitor_path);
         let vars: EnvVars = read_environment_variables();
         let workflow: Workflow = render_nxf(&globus_path, &&self.pipeline_param,  &wd.path, &namespace);
         let job = JobTemplate { header, callback, vars, workflow };
@@ -234,15 +235,14 @@ fn render_nxf(globus_path: &PathBuf, param: &PipelineParam, work_dir: &Path, nam
 }
 
 /// Render the callback using TinyTemplate
-fn render_callback(param: &PipelineParam, namespace: &PlatformNamespace) -> Callback {
+fn render_callback(param: &PipelineParam, namespace: &PlatformNamespace, monitor_path: &&PathBuf) -> Callback {
     /// included callback template
     static CALLBACK: &str = include_str!(concat!(env!("CARGO_MANIFEST_DIR"), "/data/templates/callback.txt"));
     let mut tt = TinyTemplate::new();
     tt.add_template("callback", CALLBACK).expect("Template");
     let name: &String = &param.id;
-    static WORKFLOW_MONITOR_PATH: &str = "/scratch/project_2004504/bwingfield/workflow-monitor/main.py";
     let context = CallbackContext { name: name.clone(),
-        workflow_monitor_path: WORKFLOW_MONITOR_PATH.to_string(),
+        workflow_monitor_path: monitor_path.to_string_lossy().to_string(),
         namespace: namespace.to_string()
     };
     Callback { content: tt.render("callback", &context).expect("Rendered callback") }