Implement data insertion

- Hook up external data insertion script to webserver code
- Provide rudimentary status indication
- Generalise some job creation details

1 files changed, 42 insertions, 1 deletions

diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py
index 0b87c20..70aeb6d 100644
--- a/qc_app/dbinsert.py
+++ b/qc_app/dbinsert.py
@@ -5,7 +5,6 @@ from typing import Union
 from functools import reduce
 from datetime import datetime
 
-import requests
 from redis import Redis
 from MySQLdb.cursors import DictCursor
 from flask import (
@@ -359,3 +358,45 @@ def final_confirmation():
                  "DataScale")))
     except AssertionError as aserr:
         return render_error(f"Missing data: {aserr.args[0]}")
+
+@dbinsertbp.route("/insert-data", methods=["POST"])
+def insert_data():
+    "Trigger data insertion"
+    form = request.form
+    try:
+        assert form.get("filename"), "filename"
+        assert form.get("filetype"), "filetype"
+        assert form.get("species"), "species"
+        assert form.get("genechipid"), "platform"
+        assert form.get("studyid"), "study"
+        assert form.get("datasetid"), "dataset"
+
+        filename = form["filename"]
+        filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}"
+        redisurl = app.config["REDIS_URL"]
+        if os.path.exists(filepath):
+            with Redis.from_url(redisurl, decode_responses=True) as rconn:
+                job = jobs.launch_job(
+                    jobs.data_insertion_job(
+                        rconn, filepath, form.get("filetype"),
+                        form.get("species"), form.get("genechipid"),
+                        form.get("datasetid"), app.config["SQL_URI"], redisurl,
+                        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 render_error(f"File '{filename}' no longer exists.")
+    except AssertionError as aserr:
+        return render_error(f"Missing data: {aserr.args[0]}")
+
+@dbinsertbp.route("/status/<job_id>", methods=["GET"])
+def insert_status(job_id: str):
+    "Retrieve status of data insertion."
+    with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn:
+        job = jobs.job(rconn, job_id)
+
+    if job:
+        if job["status"] == "success":
+            return render_template("insert_success.html", job=job)
+        return render_template("insert_progress.html", job=job)
+    return render_template("no_such_job.html", job_id=job_id), 400