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-rw-r--r--qc_app/dbinsert.py2
-rw-r--r--qc_app/jobs.py19
-rw-r--r--qc_app/parse.py70
-rw-r--r--qc_app/samples.py2
4 files changed, 47 insertions, 46 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 31e4cea..f36651f 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -374,7 +374,7 @@ def insert_data():
app.config["JOBS_TTL_SECONDS"]),
redisurl, f"{app.config['UPLOAD_FOLDER']}/job_errors")
- return redirect(url_for("dbinsert.insert_status", job_id=job["job_id"]))
+ return redirect(url_for("dbinsert.insert_status", job_id=job["jobid"]))
return render_error(f"File '{filename}' no longer exists.")
except AssertionError as aserr:
return render_error(f"Missing data: {aserr.args[0]}")
diff --git a/qc_app/jobs.py b/qc_app/jobs.py
index 1491015..21889da 100644
--- a/qc_app/jobs.py
+++ b/qc_app/jobs.py
@@ -29,20 +29,20 @@ def job_key(namespaceprefix: str, jobid: Union[str, UUID]) -> str:
"""Build the key by appending it to the namespace prefix."""
return f"{namespaceprefix}:{jobid}"
-def raise_jobnotfound(jobid: Union[str,UUID]):
+def raise_jobnotfound(rprefix:str, jobid: Union[str,UUID]):
"""Utility to raise a `NoSuchJobError`"""
- raise JobNotFound(f"Could not retrieve job '{jobid}'.")
+ raise JobNotFound(f"Could not retrieve job '{jobid}' from '{rprefix}.")
-def error_filename(job_id, error_dir):
+def error_filename(jobid, error_dir):
"Compute the path of the file where errors will be dumped."
- return f"{error_dir}/job_{job_id}.error"
+ return f"{error_dir}/job_{jobid}.error"
def initialise_job(# pylint: disable=[too-many-arguments]
rconn: Redis, rprefix: str, jobid: str, command: list, job_type: str,
ttl_seconds: int = 86400, extra_meta: Optional[dict] = None) -> dict:
"Initialise a job 'object' and put in on redis"
the_job = {
- "job_id": jobid, "command": shlex.join(command), "status": "pending",
+ "jobid": jobid, "command": shlex.join(command), "status": "pending",
"percent": 0, "job-type": job_type, **(extra_meta or {})
}
rconn.hset(job_key(rprefix, jobid), mapping=the_job)
@@ -95,13 +95,13 @@ def launch_job(the_job: dict, redisurl: str, error_dir):
if not os.path.exists(error_dir):
os.mkdir(error_dir)
- job_id = the_job["job_id"]
- with open(error_filename(job_id, error_dir),
+ jobid = the_job["jobid"]
+ with open(error_filename(jobid, error_dir),
"w",
encoding="utf-8") as errorfile:
subprocess.Popen( # pylint: disable=[consider-using-with]
[sys.executable, "-m", "scripts.worker", redisurl, jobsnamespace(),
- job_id],
+ jobid],
stderr=errorfile,
env={"PYTHONPATH": ":".join(sys.path)})
@@ -109,7 +109,8 @@ def launch_job(the_job: dict, redisurl: str, error_dir):
def job(rconn: Redis, rprefix: str, jobid: Union[str,UUID]):
"Retrieve the job"
- thejob = rconn.hgetall(job_key(rprefix, jobid)) or raise_jobnotfound(jobid)
+ thejob = (rconn.hgetall(job_key(rprefix, jobid)) or
+ raise_jobnotfound(rprefix, jobid))
return thejob
def update_status(
diff --git a/qc_app/parse.py b/qc_app/parse.py
index d9be993..f0c53d1 100644
--- a/qc_app/parse.py
+++ b/qc_app/parse.py
@@ -76,47 +76,47 @@ def parse():
redisurl,
f"{app.config['UPLOAD_FOLDER']}/job_errors")
- return redirect(url_for("parse.parse_status", job_id=job["job_id"]))
+ return redirect(url_for("parse.parse_status", job_id=job["jobid"]))
@parsebp.route("/status/<job_id>", methods=["GET"])
def parse_status(job_id: str):
"Retrieve the status of the job"
with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
- job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
-
- if job:
- error_filename = jobs.error_filename(
- job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
- if os.path.exists(error_filename):
- stat = os.stat(error_filename)
- if stat.st_size > 0:
- return redirect(url_for("parse.fail", job_id=job_id))
-
- job_id = job["job_id"]
- progress = float(job["percent"])
- status = job["status"]
- filename = job.get("filename", "uploaded file")
- errors = jsonpickle.decode(
- job.get("errors", jsonpickle.encode(tuple())))
- if status in ("success", "aborted"):
- return redirect(url_for("parse.results", job_id=job_id))
-
- if status == "parse-error":
+ try:
+ job = jobs.job(rconn, jobs.jobsnamespace(), job_id)
+ except jobs.JobNotFound as _exc:
+ return render_template("no_such_job.html", job_id=job_id), 400
+
+ error_filename = jobs.error_filename(
+ job_id, f"{app.config['UPLOAD_FOLDER']}/job_errors")
+ if os.path.exists(error_filename):
+ stat = os.stat(error_filename)
+ if stat.st_size > 0:
return redirect(url_for("parse.fail", job_id=job_id))
- app.jinja_env.globals.update(
- isinvalidvalue=isinvalidvalue,
- isduplicateheading=isduplicateheading)
- return render_template(
- "job_progress.html",
- job_id = job_id,
- job_status = status,
- progress = progress,
- message = job.get("message", ""),
- job_name = f"Parsing '{filename}'",
- errors=errors)
-
- return render_template("no_such_job.html", job_id=job_id), 400
+ job_id = job["jobid"]
+ progress = float(job["percent"])
+ status = job["status"]
+ filename = job.get("filename", "uploaded file")
+ errors = jsonpickle.decode(
+ job.get("errors", jsonpickle.encode(tuple())))
+ if status in ("success", "aborted"):
+ return redirect(url_for("parse.results", job_id=job_id))
+
+ if status == "parse-error":
+ return redirect(url_for("parse.fail", job_id=job_id))
+
+ app.jinja_env.globals.update(
+ isinvalidvalue=isinvalidvalue,
+ isduplicateheading=isduplicateheading)
+ return render_template(
+ "job_progress.html",
+ job_id = job_id,
+ job_status = status,
+ progress = progress,
+ message = job.get("message", ""),
+ job_name = f"Parsing '{filename}'",
+ errors=errors)
@parsebp.route("/results/<job_id>", methods=["GET"])
def results(job_id: str):
@@ -135,7 +135,7 @@ def results(job_id: str):
errors=errors,
job_name = f"Parsing '{filename}'",
user_aborted = job.get("user_aborted"),
- job_id=job["job_id"])
+ job_id=job["jobid"])
return render_template("no_such_job.html", job_id=job_id)
diff --git a/qc_app/samples.py b/qc_app/samples.py
index cf97b8d..55e94ab 100644
--- a/qc_app/samples.py
+++ b/qc_app/samples.py
@@ -255,7 +255,7 @@ def upload_samples():
redisuri,
f"{app.config['UPLOAD_FOLDER']}/job_errors")
return redirect(url_for(
- "samples.upload_status", job_id=the_job["job_id"]))
+ "samples.upload_status", job_id=the_job["jobid"]))
@samples.route("/upload/status/<uuid:job_id>", methods=["GET"])
def upload_status(job_id: uuid.UUID):