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author | Arun Isaac | 2023-12-29 18:55:37 +0000 |
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committer | Arun Isaac | 2023-12-29 19:01:46 +0000 |
commit | 204a308be0f741726b9a620d88fbc22b22124c81 (patch) | |
tree | b3cf66906674020b530c844c2bb4982c8a0e2d39 /wqflask/scripts/corr_compute.py | |
parent | 83062c75442160427b50420161bfcae2c5c34c84 (diff) | |
download | genenetwork2-204a308be0f741726b9a620d88fbc22b22124c81.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.py | 77 |
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) |