https://github.com/ReproNim/simple_workflow
Tip revision: 225f1dc06fb734ad86afb1d074b5ae2692d8b9c3 authored by Satrajit Ghosh on 09 February 2022, 21:53:23 UTC
fic: address SSL certificate error issue
fic: address SSL certificate error issue
Tip revision: 225f1dc
check_output.py
#!/usr/bin/env python
import json
import os
from glob import glob
import pandas as pd
import numpy as np
def creating_dataframe(files_list):
""" reads every json file from the files_list and creates one data frame """
outputmap = {0: 'voxels', 1: 'volume'}
df = pd.DataFrame()
for filename in files_list:
with open(filename, 'rt') as fp:
in_dict = json.load(fp)
subject = filename.split(os.path.sep)[1]
in_dict_mod = {}
for k, v in in_dict.items():
if isinstance(v, list):
for idx, value in enumerate(v):
in_dict_mod["%s_%s" % (k, outputmap[idx])] = value
else:
in_dict_mod[k] = v
df[subject] = pd.Series(in_dict_mod)
return df.T
if __name__ == "__main__":
from argparse import ArgumentParser, RawTextHelpFormatter
defstr = ' (default %(default)s)'
parser = ArgumentParser(description=__doc__,
formatter_class=RawTextHelpFormatter)
parser.add_argument("--ignoremissing", dest="nanignore", action="store_true",
default=False,
help="Ignore missing subjects when comparing")
args = parser.parse_args()
expected_files = sorted(glob('expected_output/*/segstats.json'))
if len(expected_files) < 24:
raise ValueError('Expected 24 files, but only %d files exist' % len(expected_files))
output_files = sorted(glob('output/*/segstats.json'))
if len(output_files) == 0:
raise ValueError('Output has no files')
if len(output_files) != len(expected_files):
print('Mismatch in number of expected (%d) and actual (%d) output files' % (len(expected_files),
len(output_files)))
df_exp = creating_dataframe(expected_files)
df_out = creating_dataframe(output_files)
df_exp.to_csv('output/ExpectedOutput.csv')
df_out.to_csv('output/ActualOutput.csv')
df_diff = df_exp - df_out
if args.nanignore:
df_diff = df_diff.dropna()
df_diff.to_csv('output/Difference.csv')
if np.allclose(df_diff, 0, rtol=1e-05, atol=1e-08):
print('Outputs MATCH')
else:
print('Outputs are not close enough. Printing difference')
print(df_diff)
import rdflib as rl
query = """
PREFIX nipype: <http://nipy.org/nipype/terms/>
PREFIX prov: <http://www.w3.org/ns/prov#>
SELECT DISTINCT ?platform ?fslversion
{ ?a a prov:Activity;
nipype:platform ?platform;
nipype:version ?fslversion .
FILTER (?fslversion != 'Unknown')
}
"""
prov_files = sorted(glob('expected_output/workflow_prov*.trig'))
g = rl.ConjunctiveGraph()
g.parse(prov_files[0], format='trig')
res = g.query(query)
print("Original platform: {}".format(str(res.bindings[0]['platform'])))
print("Original FSL version: {}".format(str(res.bindings[0]['fslversion'])))
prov_files = sorted(glob('output/workflow_prov*.trig'))
g = rl.ConjunctiveGraph()
g.parse(prov_files[-1], format='trig')
res = g.query(query)
for val in res.bindings:
print("Current platform: {}".format(str(val['platform'])))
print("Current FSL version: {}".format(str(val['fslversion'])))