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authorArun Isaac2023-12-29 18:55:37 +0000
committerArun Isaac2023-12-29 19:01:46 +0000
commit204a308be0f741726b9a620d88fbc22b22124c81 (patch)
treeb3cf66906674020b530c844c2bb4982c8a0e2d39 /wqflask/scripts/corr_compute.py
parent83062c75442160427b50420161bfcae2c5c34c84 (diff)
downloadgenenetwork2-204a308be0f741726b9a620d88fbc22b22124c81.tar.gz
Namespace all modules under gn2.
We move all modules under a gn2 directory. This is important for "correct" packaging and deployment as a Guix service.
Diffstat (limited to 'wqflask/scripts/corr_compute.py')
-rw-r--r--wqflask/scripts/corr_compute.py77
1 files changed, 0 insertions, 77 deletions
diff --git a/wqflask/scripts/corr_compute.py b/wqflask/scripts/corr_compute.py
deleted file mode 100644
index 34c3ad54..00000000
--- a/wqflask/scripts/corr_compute.py
+++ /dev/null
@@ -1,77 +0,0 @@
-"""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
- 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)