From 7976230ffcb1de4f744895ee252298dea9a15f4c Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 23 Jan 2024 12:33:08 +0300
Subject: Update scripts to use redis prefix.

---
 qc_app/jobs.py         | 19 ++++++++++++++++++-
 qc_app/upload/rqtl2.py | 37 ++++++++++++++++++++-----------------
 2 files changed, 38 insertions(+), 18 deletions(-)

(limited to 'qc_app')

diff --git a/qc_app/jobs.py b/qc_app/jobs.py
index dc1f967..cf4e4ef 100644
--- a/qc_app/jobs.py
+++ b/qc_app/jobs.py
@@ -97,7 +97,8 @@ def launch_job(the_job: dict, redisurl: str, error_dir):
               "w",
               encoding="utf-8") as errorfile:
         subprocess.Popen( # pylint: disable=[consider-using-with]
-            [sys.executable, "-m", "scripts.worker", redisurl, job_id],
+            [sys.executable, "-m", "scripts.worker", redisurl, jobsnamespace(),
+             job_id],
             stderr=errorfile,
             env={"PYTHONPATH": ":".join(sys.path)})
 
@@ -107,3 +108,19 @@ def job(rconn: Redis, rprefix: str, jobid: Union[str,UUID]):
     "Retrieve the job"
     thejob = rconn.hgetall(job_key(rprefix, jobid)) or raise_jobnotfound(jobid)
     return thejob
+
+def update_status(
+        rconn: Redis, rprefix: str, jobid: Union[str, UUID], status: str):
+    """Update status of job in redis."""
+    rconn.hset(name=job_key(rprefix, jobid), key="status", value=status)
+
+def update_stdout_stderr(rconn: Redis,
+                         rprefix: str,
+                         jobid: Union[str, UUID],
+                         bytes_read: bytes,
+                         stream: str):
+    "Update the stdout/stderr keys according to the value of `stream`."
+    thejob = job(rconn, rprefix, jobid)
+    contents = thejob.get(stream, '')
+    new_contents = contents + bytes_read.decode("utf-8")
+    rconn.hset(name=job_key(rprefix, jobid), key=stream, value=new_contents)
diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 7805114..eea49e1 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -552,11 +552,13 @@ def confirm_bundle_details(species_id: int, population_id: int):
         _job = jobs.launch_job(
             jobs.initialise_job(
                 rconn,
+                jobs.jobsnamespace(),
                 jobid,
                 [
                     sys.executable, "-m", "scripts.process_rqtl2_bundle",
-                    app.config["SQL_URI"], app.config["REDIS_URL"], jobid,
-                    "--redisexpiry", str(redis_ttl_seconds)],
+                    app.config["SQL_URI"], app.config["REDIS_URL"],
+                    jobs.jobsnamespace(), jobid, "--redisexpiry",
+                    str(redis_ttl_seconds)],
                 "R/qtl2 Bundle Upload",
                 redis_ttl_seconds,
                 {
@@ -588,21 +590,22 @@ def confirm_bundle_details(species_id: int, population_id: int):
 def rqtl2_processing_status(jobid: UUID):
     """Retrieve the status of the job processing the uploaded R/qtl2 bundle."""
     with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
-        thejob = jobs.job(rconn, jobid)
-        if not bool(thejob):
-            return render_template("rqtl2/no-such-job.html", jobid=jobid)
+        try:
+            thejob = jobs.job(rconn, jobs.jobsnamespace(), jobid)
 
-        messagelistname = thejob.get("log-messagelist")
-        logmessages = (rconn.lrange(messagelistname, 0, -1)
-                       if bool(messagelistname) else [])
+            messagelistname = thejob.get("log-messagelist")
+            logmessages = (rconn.lrange(messagelistname, 0, -1)
+                           if bool(messagelistname) else [])
 
-        if thejob["status"] == "error":
-            return render_template(
-                "rqtl2/rqtl2-job-error.html", job=thejob, messages=logmessages)
-        if thejob["status"] == "success":
-            return render_template("rqtl2/rqtl2-job-results.html",
-                                   job=thejob,
-                                   messages=logmessages)
+            if thejob["status"] == "error":
+                return render_template(
+                    "rqtl2/rqtl2-job-error.html", job=thejob, messages=logmessages)
+            if thejob["status"] == "success":
+                return render_template("rqtl2/rqtl2-job-results.html",
+                                       job=thejob,
+                                       messages=logmessages)
 
-        return render_template(
-            "rqtl2/rqtl2-job-status.html", job=thejob, messages=logmessages)
+            return render_template(
+                "rqtl2/rqtl2-job-status.html", job=thejob, messages=logmessages)
+        except jobs.JobNotFound as _exc:
+            return render_template("rqtl2/no-such-job.html", jobid=jobid)
-- 
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