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[Code review] Code style and module requirements. #2

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[Code review] Code style and module requirements. #2

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fa4fff5
[ADD] `requirements.txt` file.
mathdugre Sep 24, 2021
eb076e0
[REACTOR] Remove unused import and fix style to PEP 8.
mathdugre Sep 24, 2021
6938b92
[REMOVE] Commented code.
mathdugre Sep 24, 2021
61f2de9
[REFACTOR] Move the docstring within the function body.
mathdugre Sep 24, 2021
a6cd83d
[REFACTOR] format code base with psf/black.
mathdugre Sep 24, 2021
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145 changes: 86 additions & 59 deletions NeuroCI.py
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Original file line number Diff line number Diff line change
@@ -1,56 +1,83 @@
import requests
import yaml
import json
import datetime
import sys
import os
#from github import Github
from ast import literal_eval
import time
import datetime

from cbrainAPI import *
from cacheOps import *
import yaml

from cacheOps import (
download_cache,
populate_cache_filenames,
update_statuses,
pipeline_manager,
populate_results,
)
from cbrainAPI import cbrain_login, cbrain_logout, cbrain_get_all_tasks

##################################################################################

def main(cbrain_token, CCI_token, experiment_definition, cbrain_ids, latest_artifacts_url):

for dataset in experiment_definition['Datasets']:

download_cache(dataset + '.json', CCI_token, latest_artifacts_url) #Downloads newest cache to json file
print('Downloaded newest cache for: ' + dataset + '.json')

task_list = cbrain_get_all_tasks(cbrain_token) #Gets the complete list of tasks for the user on CBRAIN
print('Fetched the list of tasks for the CBRAIN user')

start = time.time()
update_statuses(dataset + '.json', task_list) #Updates the contents of a cache to reflect CBRAIN task statuses
end = time.time()
print('Updated statuses in cache for: ' + dataset + '.json in' + str(datetime.timedelta(seconds=(end - start))))

for pipeline in experiment_definition['Pipelines']:

start = time.time()
populate_cache_filenames(dataset + '.json', cbrain_token, experiment_definition['Datasets'][dataset]['Blocklist'], pipeline, cbrain_ids['Data_Provider_IDs'][dataset], experiment_definition) #Populates a cache with any new files found
end = time.time()
print('Populated cache filenames for: ' + dataset + '.json' + ', ' + pipeline + " in" + str(datetime.timedelta(seconds=(end - start))))

pipeline_manager(cbrain_token, experiment_definition, cbrain_ids, pipeline, dataset)
print('Posted tasks for: ' + dataset + '.json' + ', ' + pipeline)

populate_results(dataset + '.json', cbrain_token)
print('Populated results for ' + dataset + '.json')
#extract_results()
#analysis(expdef[script])

#start = time.time()
#update_statuses(dataset + '.json', cbrain_token)
#end = time.time()
#print('Updated statuses in cache for: ' + dataset + '.json in' + str(datetime.timedelta(seconds=(end - start))))

def main(
cbrain_token, CCI_token, experiment_definition, cbrain_ids, latest_artifacts_url
):

for dataset in experiment_definition["Datasets"]:

download_cache(
dataset + ".json", CCI_token, latest_artifacts_url
) # Downloads newest cache to json file
print("Downloaded newest cache for: " + dataset + ".json")

task_list = cbrain_get_all_tasks(
cbrain_token
) # Gets the complete list of tasks for the user on CBRAIN
print("Fetched the list of tasks for the CBRAIN user")

start = time.time()
update_statuses(
dataset + ".json", task_list
) # Updates the contents of a cache to reflect CBRAIN task statuses
end = time.time()
print(
"Updated statuses in cache for: "
+ dataset
+ ".json in"
+ str(datetime.timedelta(seconds=(end - start)))
)

for pipeline in experiment_definition["Pipelines"]:

start = time.time()
populate_cache_filenames(
dataset + ".json",
cbrain_token,
experiment_definition["Datasets"][dataset]["Blocklist"],
pipeline,
cbrain_ids["Data_Provider_IDs"][dataset],
experiment_definition,
) # Populates a cache with any new files found
end = time.time()
print(
"Populated cache filenames for: "
+ dataset
+ ".json"
+ ", "
+ pipeline
+ " in"
+ str(datetime.timedelta(seconds=(end - start)))
)

pipeline_manager(
cbrain_token, experiment_definition, cbrain_ids, pipeline, dataset
)
print("Posted tasks for: " + dataset + ".json" + ", " + pipeline)

populate_results(dataset + ".json", cbrain_token)
print("Populated results for " + dataset + ".json")


##################################################################################

#Obtain login credentials from args, stored in CI environment variables.
# Obtain login credentials from args, stored in CI environment variables.

cbrain_user = sys.argv[1]
cbrain_password = sys.argv[2]
Expand All @@ -60,22 +87,24 @@ def main(cbrain_token, CCI_token, experiment_definition, cbrain_ids, latest_arti

##################################################################################

#Main code execution section
# Main code execution section

with open('Experiment_Definition.yaml') as file: #Load experiment definition
try:
experiment_definition = yaml.safe_load(file)
except yaml.YAMLError as exception: #yaml file not valid
print('The Experiment Definition file is not valid')
print(exception)
with open("Experiment_Definition.yaml") as file: # Load experiment definition
try:
experiment_definition = yaml.safe_load(file)
except yaml.YAMLError as exception: # yaml file not valid
print("The Experiment Definition file is not valid")
print(exception)


with open('./Config_Files/CBRAIN_IDs.yaml') as file: #Load mappings for all CBRAIN DP_IDs and toolconfig IDs
try:
cbrain_ids = yaml.safe_load(file)
except yaml.YAMLError as exception: #yaml file not valid
print('The configuration file is not valid')
print(exception)
with open(
"./Config_Files/CBRAIN_IDs.yaml"
) as file: # Load mappings for all CBRAIN DP_IDs and toolconfig IDs
try:
cbrain_ids = yaml.safe_load(file)
except yaml.YAMLError as exception: # yaml file not valid
print("The configuration file is not valid")
print(exception)

print("Using artifacts from : " + latest_artifacts_url)

Expand All @@ -85,5 +114,3 @@ def main(cbrain_token, CCI_token, experiment_definition, cbrain_ids, latest_arti

cbrain_logout(cbrain_token)
##################################################################################


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