Update Web-UI: use new error collection paradigm

- README.org: document how to run scripts manually
- manifest.scm: remove python-rq as a dependency
- qc_app/jobs.py: rework job launching and processing
- qc_app/parse.py: use reworked job processing
- qc_app/templates/job_progress.html: display progress correctly
- qc_app/templates/parse_results.html: display final results
- scripts/worker.py: new worker script

1 files changed, 71 insertions, 166 deletions

diff --git a/qc_app/parse.py b/qc_app/parse.py
index baad9a6..d2fa030 100644
--- a/qc_app/parse.py
+++ b/qc_app/parse.py
@@ -1,10 +1,9 @@
 """File parsing module"""
 import os
-import sqlite3
 from functools import reduce
 
+import jsonpickle
 from redis import Redis
-from rq import get_current_job
 from flask import (
     request,
     url_for,
@@ -14,50 +13,13 @@ from flask import (
     current_app as app)
 
 from . import jobs
-from quality_control.errors import ParseError
+from quality_control.errors import InvalidValue
 from quality_control.parsing import (
     FileType,
-    parse_file,
-    strain_names,
-    parse_errors)
+    strain_names)
 
 parsebp = Blueprint("parse", __name__)
 
-def queued_parse(
-        filepath: str, filetype: FileType, strainsfile: str, redis_url: str,
-        dbpath: str):
-    job = get_current_job()
-    job_id = job.get_id()
-    with Redis.from_url(redis_url) as rconn:
-        dbconn = sqlite3.connect(dbpath)
-        try:
-            job_meta = jobs.update_meta(
-                dbconn, job_id, status = "in-progress", progress = 0)
-            parsed = parse_file(filepath, filetype, strain_names(strainsfile))
-            for line, curr_size in parsed:
-                job_meta = jobs.update_meta(
-                    dbconn, job_id,
-                    progress=((curr_size/job_meta["filesize"]) * 100),
-                    message = f"Parsed {curr_size} bytes")
-
-            os.remove(filepath)
-            jobs_meta = jobs.update_meta(
-                dbconn, job_id, progress = 100, status = "success",
-                message = "no errors found")
-        except ParseError as pe:
-            pe_dict = pe.args[0]
-            job_meta = jobs.update_meta(
-                dbconn, job_id, status = "parse-error", results = {
-                    "filename": os.path.basename(filepath), "filetype": filetype,
-                    "position": pe_dict["position"],
-                    "line_number": pe_dict["line_number"]
-                })
-        finally:
-            dbconn.close()
-
-def retrieve_dbpath():
-    return os.path.join(app.config["UPLOAD_FOLDER"], "jobs.db")
-
 @parsebp.route("/parse", methods=["GET"])
 def parse():
     """Trigger file parsing"""
@@ -73,6 +35,10 @@ def parse():
         flash("No filetype provided", "alert-error")
         errors = True
 
+    if filetype not in ("average", "standard-error"):
+        flash("Invalid filetype provided", "alert-error")
+        errors = True
+
     filepath = os.path.join(app.config["UPLOAD_FOLDER"], filename)
     if not os.path.exists(filepath):
         flash("Selected file does not exist (any longer)", "alert-danger")
@@ -81,144 +47,83 @@ def parse():
     if errors:
         return redirect(url_for("entry.index"))
 
-    jobs.create_jobs_table(retrieve_dbpath())
-    filetype = (
-        FileType.AVERAGE if filetype == "average" else FileType.STANDARD_ERROR)
-    job = jobs.enqueue_job(
-        "qc_app.parse.queued_parse", filepath, filetype,
-        os.path.join(os.getcwd(), "etc/strains.csv"), app.config["REDIS_URL"],
-        retrieve_dbpath())
-    try:
-        dbconn = sqlite3.connect(retrieve_dbpath())
-        jobs.update_meta(
-            dbconn, job.get_id(), filename=filename, filesize=os.stat(filepath).st_size,
-            status="enqueued", progress=0)
-    except Exception as exc:
-        import traceback
-        print(traceback.format_exc())
-        dbconn.rollback()
-    finally:
-        dbconn.close()
-
-    return redirect(url_for("parse.parse_status", job_id=job.get_id()))
+    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+        job = jobs.launch_job(
+            rconn, filepath, filetype, app.config["REDIS_URL"],
+        f"{app.config['UPLOAD_FOLDER']}/job_errors")
+
+    return redirect(url_for("parse.parse_status", job_id=job["job_id"]))
 
 @parsebp.route("/status/<job_id>", methods=["GET"])
 def parse_status(job_id: str):
-    try:
-        dbconn = sqlite3.connect(retrieve_dbpath(), timeout=10)
-        job = jobs.job(job_id)
-        if job:
-            job_id = job.get_id()
-            job_meta = jobs.retrieve_meta(dbconn, job_id)
-            progress = job_meta["progress"]
-            status = job_meta["status"]
-            filename = job_meta.get("filename", "uploaded file")
-            if status == "success":
-                return redirect(url_for("parse.results", job_id=job_id))
-
-            if status == "parse-error":
+    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+        job = jobs.job(rconn, 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))
 
-            return render_template(
-                "job_progress.html",
-                job_id = job_id,
-                job_status = status,
-                progress = progress,
-                message = job_meta.get("message", ""),
-                job_name = f"Parsing '{filename}'")
-
-        return render_template("no_such_job.html", job_id=job_id)
-    except sqlite3.OperationalError:
-        return redirect(url_for("parse.parse_status", job_id=job_id))
-    except Exception as exc:
-        import traceback
-        print(traceback.format_exc())
-        return exc
-    finally:
-        dbconn.close()
+        print(f"THE JOB {job}")
+        job_id = job["job_id"]
+        progress = float(job["percent"])
+        status = job["status"]
+        filename = job.get("filename", "uploaded file")
+        if status == "success":
+            return redirect(url_for("parse.results", job_id=job_id))
+
+        if status == "parse-error":
+            return redirect(url_for("parse.fail", job_id=job_id))
+
+        return render_template(
+            "job_progress.html",
+            job_id = job_id,
+            job_status = status,
+            progress = progress,
+            message = job.get("message", ""),
+            job_name = f"Parsing '{filename}'")
+
+    return render_template("no_such_job.html", job_id=job_id)
 
 @parsebp.route("/results/<job_id>", methods=["GET"])
 def results(job_id: str):
     """Show results of parsing..."""
-    job = jobs.job(job_id)
+    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+        job = jobs.job(rconn, job_id)
+
     if job:
-        try:
-            dbconn = sqlite3.connect(retrieve_dbpath())
-            job_meta = jobs.retrieve_meta(dbconn, job_id)
-            filename = job_meta["filename"]
-            errors = job_meta.get("errors", [])
-            return render_template(
-                "parse_results.html",
-                errors=errors,
-                job_name = f"Parsing '{filename}'",
-                starting_line_number=job_meta.get("starting_line_number", 0))
-        except Exception as exc:
-            import traceback
-            print(traceback.format_exc())
-        finally:
-            dbconn.close()
+        filename = job["filename"]
+        errors = jsonpickle.decode(job["errors"])
+        return render_template(
+            "parse_results.html",
+            errors=errors,
+            job_name = f"Parsing '{filename}'",
+            isinvalidvalue=lambda item: isinstance(item, InvalidValue))
 
     return render_template("no_such_job.html", job_id=job_id)
 
-def queued_collect_errors(
-        filepath: str, filetype: FileType, strainsfile: str, redis_url: str,
-        dbpath: str, seek_pos: int = 0):
-    job = get_current_job()
-    job_id = job.get_id()
-    errors = []
-    count = 0
-    with Redis.from_url(redis_url) as rconn:
-        try:
-            dbconn = sqlite3.connect(dbpath)
-            job_meta = jobs.retrieve_meta(dbconn, job.get_id())
-            for error in parse_errors(
-                    filepath, filetype, strain_names(strainsfile),
-                    seek_pos):
-                count = count + 1
-                progress  = ((error["position"] / job_meta["filesize"]) * 100)
-                job_meta = jobs.update_meta(
-                    dbconn, job_id, message = f"Collected {count} errors",
-                    progress = progress)
-                errors.append(error)
-
-            job_meta = jobs.update_meta(
-                dbconn, job_id, errors = errors, progress = 100, status = "success")
-            os.remove(filepath)
-        except Exception as exc:
-            dbconn.rollback()
-        finally:
-            dbconn.close()
-
 @parsebp.route("/fail/<job_id>", methods=["GET"])
 def fail(job_id: str):
     """Handle parsing failure"""
-    try:
-        dbpath = retrieve_dbpath()
-        dbconn = sqlite3.connect(dbpath)
-        old_job = jobs.job(job_id)
-        if old_job:
-            job_id = old_job.get_id()
-            old_meta = jobs.retrieve_meta(dbconn, job_id)
-            progress = old_meta["progress"]
-            status = old_meta["status"]
-            results = old_meta["results"]
-            filename = old_meta["filename"]
-
-            new_job = jobs.enqueue_job(
-                "qc_app.parse.queued_collect_errors",
-                os.path.join(
-                    app.config["UPLOAD_FOLDER"], old_meta["filename"]),
-                results["filetype"], os.path.join(os.getcwd(), "etc/strains.csv"),
-                app.config["REDIS_URL"], dbpath, results["position"])
-            jobs.update_meta(
-                dbconn, new_job.get_id(), status =  "Collecting Errors",
-                filename = old_meta["filename"], filesize = old_meta["filesize"],
-                starting_line_number = results["line_number"],
-                progress = progress)
-            return redirect(url_for("parse.parse_status", job_id=new_job.get_id()))
-
-        return render_template("no_such_job.html", job_id=job_id)
-    except Exception as exc:
-        dbconn.rollback()
-    finally:
-        dbconn.close()
+    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+        old_job = jobs.job(rconn, job_id)
+
+    if old_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:
+                with open(error_filename) as errorfile:
+                    return errorfile.read()
+
+        # job_id = old_job["job_id"]
+        progress = old_job["progress"]
+        status = old_job["status"]
+        results = old_job["results"]
+        filename = old_job["filename"]
+
+    return render_template("no_such_job.html", job_id=job_id)