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-rw-r--r--wqflask/scripts/corr_compute.py78
-rw-r--r--wqflask/wqflask/templates/loading_corrs.html28
-rw-r--r--wqflask/wqflask/views.py59
3 files changed, 148 insertions, 17 deletions
diff --git a/wqflask/scripts/corr_compute.py b/wqflask/scripts/corr_compute.py
new file mode 100644
index 00000000..c98a66a4
--- /dev/null
+++ b/wqflask/scripts/corr_compute.py
@@ -0,0 +1,78 @@
+"""Compute the correlations."""
+
+import sys
+import json
+import pickle
+import pathlib
+import datetime
+
+from flask import g
+
+from wqflask import app
+from wqflask.user_session import UserSession
+from wqflask.correlation.show_corr_results import set_template_vars
+from wqflask.correlation.correlation_gn3_api import compute_correlation
+
+class UserSessionSimulator():
+
+ def __init__(self, user_id):
+ self._user_id = user_id
+
+ @property
+ def user_id(self):
+ return self._user_id
+
+error_types = {
+ "WrongCorrelationType": "Wrong Correlation Type",
+ "CalledProcessError": "Called Process Error"
+}
+
+def e_time():
+ return datetime.datetime.utcnow().isoformat()
+
+def compute(form):
+ import subprocess
+ from gn3.settings import CORRELATION_COMMAND
+ try:
+ correlation_results = compute_correlation(form, compute_all=True)
+ except Exception as exc:
+ return {
+ "error-type": error_types[type(exc).__name__],
+ "error-message": exc.args[0]
+ }
+
+ return set_template_vars(form, correlation_results)
+
+if __name__ == "__main__":
+ ARGS_COUNT = 3
+ if len(sys.argv) < ARGS_COUNT:
+ print(f"{e_time()}: You need to pass the file with the picked form",
+ file=sys.stderr)
+ sys.exit(1)
+
+ if len(sys.argv) > ARGS_COUNT:
+ print(f"{e_time()}: Unknown arguments {sys.argv[ARGS_COUNT:]}",
+ file=sys.stderr)
+ sys.exit(1)
+
+ filepath = pathlib.Path(sys.argv[1])
+ if not filepath.exists():
+ print(f"File not found '{filepath}'", file=sys.stderr)
+ sys.exit(2)
+
+ with open(filepath, "rb") as pfile:
+ form = pickle.Unpickler(pfile).load()
+
+ with app.app_context():
+ g.user_session = UserSessionSimulator(sys.argv[2])
+ results = compute(form)
+
+ print(json.dumps(results), file=sys.stdout)
+
+ if "error-type" in results:
+ print(
+ f"{results['error-type']}: {results['error-message']}",
+ file=sys.stderr)
+ sys.exit(3)
+
+ sys.exit(0)
diff --git a/wqflask/wqflask/templates/loading_corrs.html b/wqflask/wqflask/templates/loading_corrs.html
new file mode 100644
index 00000000..8abd5464
--- /dev/null
+++ b/wqflask/wqflask/templates/loading_corrs.html
@@ -0,0 +1,28 @@
+<!DOCTYPE html>
+<html>
+
+ <head>
+ <title>Loading Correlation Results</title>
+
+ <meta charset="utf-8" />
+ <meta http-equiv="refresh" content="5">
+
+ <link rel="stylesheet" type="text/css"
+ href="{{url_for('css', filename='bootstrap/css/bootstrap.css')}}" />
+ <link rel="stylesheet" type="text/css"
+ href="/static/new/css/bootstrap-custom.css" />
+ </head>
+
+ <body>
+ <div style="margin: 0; position: absolute; top: 50%; left: 50%; transform: translate(-50%, -50%);">
+ <h1>&nbsp;Correlation Computation in progress ...</h1>
+ <div style="text-align: center;">
+ <img align="center" src="/static/gif/waitAnima2.gif">
+ </div>
+ </div>
+
+ <script src="{{ url_for('js', filename='jquery/jquery.min.js') }}" type="text/javascript"></script>
+ <script src="{{ url_for('js', filename='bootstrap/js/bootstrap.min.js') }}" type="text/javascript"></script>
+ </body>
+
+</html>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 0d8e5e64..211a8f13 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -19,6 +19,8 @@ import xlsxwriter
from zipfile import ZipFile
from zipfile import ZIP_DEFLATED
+from uuid import UUID
+
from wqflask import app
from gn3.computations.gemma import generate_hash_of_string
@@ -31,6 +33,7 @@ from flask import render_template
from flask import send_from_directory
from flask import redirect
from flask import send_file
+from flask import url_for
# Some of these (like collect) might contain endpoints, so they're still used.
# Blueprints should probably be used instead.
@@ -71,6 +74,7 @@ from wqflask.db_info import InfoPage
from utility import temp_data
from utility.tools import TEMPDIR
from utility.tools import USE_REDIS
+from utility.tools import REDIS_URL
from utility.tools import GN_SERVER_URL
from utility.tools import GN_VERSION
from utility.tools import JS_TWITTER_POST_FETCHER_PATH
@@ -78,11 +82,16 @@ from utility.tools import JS_GUIX_PATH
from utility.helper_functions import get_species_groups
from utility.redis_tools import get_redis_conn
+import utility.hmac as hmac
+
+from base.webqtlConfig import TMPDIR
from base.webqtlConfig import GENERATED_IMAGE_DIR
from wqflask.database import database_connection
+import jobs.jobs as jobs
+
Redis = get_redis_conn()
@@ -822,24 +831,40 @@ def __handle_correlation_error__(exc):
"error-message": exc.args[0]
})
-@app.route("/corr_compute", methods=('POST',))
+@app.route("/corr_compute", methods=('POST', 'GET'))
def corr_compute_page():
- import subprocess
- from gn3.settings import CORRELATION_COMMAND
- try:
- correlation_results = compute_correlation(
- request.form, compute_all=True)
- except WrongCorrelationType as exc:
- return __handle_correlation_error__(exc)
- except subprocess.CalledProcessError as cpe:
- actual_command = (
- os.readlink(CORRELATION_COMMAND)
- if os.path.islink(CORRELATION_COMMAND)
- else CORRELATION_COMMAND)
- raise Exception(actual_command, cpe.output, cpe.stdout, cpe.stderr) from cpe
-
- correlation_results = set_template_vars(request.form, correlation_results)
- return render_template("correlation_page.html", **correlation_results)
+ with Redis.from_url(REDIS_URL, decode_responses=True) as rconn:
+ if request.method == "POST":
+ request_received = datetime.datetime.utcnow()
+ filename=hmac.hmac_creation(f"request_form_{request_received.isoformat()}")
+ filepath = f"{TMPDIR}{filename}"
+ with open(filepath, "wb") as pfile:
+ pickle.dump(request.form, pfile, protocol=pickle.HIGHEST_PROTOCOL)
+ job_id = jobs.queue(
+ rconn, {
+ "command": [
+ sys.executable, "-m", "scripts.corr_compute", filepath,
+ g.user_session.user_id],
+ "request_received_time": request_received.isoformat(),
+ "status": "queued"
+ })
+ jobs.run(job_id, REDIS_URL)
+
+ return redirect(url_for("corr_compute_page", job_id=str(job_id)))
+
+ job = jobs.job(
+ rconn, UUID(request.args.get("job_id"))).maybe(
+ {}, lambda the_job: the_job)
+
+ if jobs.completed_successfully(job):
+ output = json.loads(job.get("stdout", "{}"))
+ return render_template("correlation_page.html", **output)
+
+ if jobs.completed_erroneously(job):
+ output = json.loads(job.get("stdout", "{}"))
+ return render_template("correlation_error_page.html", error=output)
+
+ return render_template("loading_corrs.html")
@app.route("/corr_matrix", methods=('POST',))