From d02cef83c3c0b3f3098df1a7e7eeaf90430f784a Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 8 Feb 2024 15:54:32 +0300
Subject: R/qtl2 QC: Set up scaffolding for QC UI

Set up the scaffolding for the flows and UI that will be used when
running QC against the uploaded R/qtl2 bundle.

This will be fleshed out later, and the UI is likely to change
somewhat, down the line.
---
 qc_app/upload/rqtl2.py | 63 +++++++++++++++++++++++++++++++++++---------------
 1 file changed, 45 insertions(+), 18 deletions(-)

(limited to 'qc_app/upload')

diff --git a/qc_app/upload/rqtl2.py b/qc_app/upload/rqtl2.py
index 9d787e1..afe0c2e 100644
--- a/qc_app/upload/rqtl2.py
+++ b/qc_app/upload/rqtl2.py
@@ -18,8 +18,6 @@ from flask import (
     current_app as app)
 
 from r_qtl import r_qtl2
-from r_qtl import r_qtl2_qc as rqc
-from r_qtl.errors import InvalidFormat
 
 from qc_app import jobs
 from qc_app.files import save_file, fullpath
@@ -135,12 +133,6 @@ class __RequestError__(Exception): #pylint: disable=[invalid-name]
     methods=["GET", "POST"])
 def upload_rqtl2_bundle(species_id: int, population_id: int):
     """Allow upload of R/qtl2 bundle."""
-    this_page_with_errors = redirect(url_for("upload.rqtl2.upload_rqtl2_bundle",
-                                             species_id=species_id,
-                                             population_id=population_id,
-                                             pgsrc="error"),
-                                     code=307)
-
     with database_connection(app.config["SQL_URI"]) as conn:
         species = species_by_id(conn, species_id)
         population = population_by_species_and_id(
@@ -171,17 +163,52 @@ def upload_rqtl2_bundle(species_id: int, population_id: int):
         if not is_zipfile(str(the_file)):
             raise __RequestError__("Invalid file! Expected a zip file.")
 
+        redisuri = app.config["REDIS_URL"]
+        with Redis.from_url(redisuri, decode_responses=True) as rconn:
+            jobid = str(uuid4())
+            redis_ttl_seconds = app.config["JOBS_TTL_SECONDS"]
+            jobs.launch_job(
+                jobs.initialise_job(
+                    rconn,
+                    jobs.jobsnamespace(),
+                    jobid,
+                    [sys.executable, "-m", "scripts.qc_on_rqtl2_bundle",
+                    app.config["SQL_URI"], app.config["REDIS_URL"],
+                    jobs.jobsnamespace(), jobid, "--redisexpiry",
+                    str(redis_ttl_seconds)],
+                    "rqtl2-bundle-qc-job",
+                    redis_ttl_seconds,
+                    {}),
+                redisuri,
+                f"{app.config['UPLOAD_FOLDER']}/job_errors")
+            return redirect(url_for(
+                "upload.rqtl2.rqtl2_bundle_qc_status", jobid=jobid))
+
+@rqtl2.route("/upload/species/rqtl2-bundle/qc-status/<uuid:jobid>",
+             methods=["GET", "POST"])
+def rqtl2_bundle_qc_status(jobid: UUID):
+    """Check the status of the QC jobs."""
+    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
         try:
-            with ZipFile(str(the_file), "r") as zfile:
-                rqc.validate_bundle(zfile)
-                return render_template(
-                    "rqtl2/upload-rqtl2-bundle-step-02.html",
-                    species=species,
-                    population=population,
-                    rqtl2_bundle_file=the_file.name)#type: ignore[union-attr]
-        except (InvalidFormat, __RequestError__) as exc:
-            flash("".join(exc.args), "alert-error error-rqtl2")
-            return this_page_with_errors
+            thejob = jobs.job(rconn, jobs.jobsnamespace(), jobid)
+            messagelistname = thejob.get("log-messagelist")
+            logmessages = (rconn.lrange(messagelistname, 0, -1)
+                           if bool(messagelistname) else [])
+            jobstatus = thejob["status"]
+            if jobstatus == "error":
+                return render_template("rqtl2/rqtl2-qc-job-error.html",
+                                       job=thejob,
+                                       messages=logmessages)
+            if jobstatus == "success":
+                return render_template("rqtl2/rqtl2-qc-job-results.html",
+                                       job=thejob,
+                                       messages=logmessages)
+
+            return render_template("rqtl2/rqtl2-qc-job-status.html",
+                                   job=thejob,
+                                   messages=tuple())
+        except jobs.JobNotFound:
+            return render_template("rqtl2/no-such-job.html", jobid=jobid)
 
 def check_errors(conn, *args, **kwargs):#pylint: disable=[too-many-return-statements]
     """Check for select errors in the forms and return a page to redirect to."""
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