replace callback with workflow-monitor

data/templates/callback.txt

 
-# set up reporting job status to INTERVENE backend
-
-# need to escape starting curly bracket to prevent templating error
-# (the comment above only makes sense in the original template file)
-callback_exit_handler() \{
-  # report the status of the job to the INTERVENE backend
-  exit_code=$?
-
-  if [ $exit_code -eq 0 ]; then
-      body='\{"status": "COMPLETED", "pipelineId": "{name}", "outdir": ""}'
-  else
-      body='\{"status": "FAILED", "pipelineId": "{name}", "outdir": ""}'
-  fi
-
-  # do a callback
-  url="https://dev.intervenegeneticscores.org/pipeline-manager/pipeline/csc/notify"
-  # escaping json is a pain
-  echo $body > callback.txt
-
-  curl -X POST -H "Content-Type: application/json" -H "Authorization: Basic $CALLBACK_TOKEN" --data @callback.txt $url
-
-  exit $exit_code
-}
-
 # run everything in "strict mode". error early, error often!
 set -euxo pipefail
 
-trap callback_exit_handler EXIT
+# set up reporting job status to INTERVENE backend
+
+# dependencies for workflow-monitor (python3.10 & requests library)
+module load python-data/3.10-23.07
+
+# run the monitor in the background
+python3 {workflow_monitor_path} &
 
 # ------------------------------------------------------------------------------
 

data/templates/nxf.txt

 
 # time to start doing work!
 
-# step 0. load dependencies
+# load dependencies
 # (curl, jq, and singularity/apptainer are preloaded on Puhti)
 module load nextflow/22.10.1
 module load parallel
 
-# step 1: transfer data in parallel
+# transfer data in parallel
 parallel --col-sep ' ' \
   -a {work_dir}/{name}/transfer.txt \
   java -Xmx256m \
@@ -23,7 +23,7 @@ set_tmpdir() \{
 
 set_tmpdir
 
-# step 2: run pgsc_calc and calculate some scores
+# run pgsc_calc and calculate some scores!
 nextflow run {pgsc_calc_dir} -profile singularity \
          -c {work_dir}/{name}/allas.config \
          -params-file {work_dir}/{name}/params.json \
@@ -32,9 +32,8 @@ nextflow run {pgsc_calc_dir} -profile singularity \
          --min_overlap 0.01 \
          --max_cpus 40 \
          --max_memory "32.GB" \
-         --parallel 
-
-# step 3: report job status to INTERVENE platform
-# (automatically executed in callback_exit_handler by trap)
+         --parallel \
+         -with-weblog http://localhost:8000 \
+         -name {name}
 
 # ------------------------------------------------------------------------------

src/slurm/job.rs

@@ -157,6 +157,7 @@ struct NextflowContext {
 #[derive(Serialize)]
 struct CallbackContext {
     name: String,
+    workflow_monitor_path: String
 }
 
 /// Write nextflow parameters to working directory
@@ -236,7 +237,9 @@ fn render_callback(param: &PipelineParam) -> Callback {
     let mut tt = TinyTemplate::new();
     tt.add_template("callback", CALLBACK).expect("Template");
     let name: &String = &param.id;
-    let context = CallbackContext { name: name.clone() };
+    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() };
     Callback { content: tt.render("callback", &context).expect("Rendered callback") }
 }