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import json
import os
import sys
# Required Evils!
from flask import g
from wqflask import app
from wqflask.show_trait import show_trait
from wqflask.database import database_connection
from wqflask.search_results import SearchResultPage
class UserSessionSimulator():
def __init__(self, user_id):
self._user_id = user_id
@property
def user_id(self):
return self._user_id
def dump_sample_data(dataset_name, trait_id):
"""Given a DATASET_NAME e.g. 'BXDPublish' and a TRAIT_ID
e.g. '10007', dump the sample data as json object"""
with database_connection() as conn, conn.cursor() as cursor:
sample_data = {"headers": ["Name", "Value", "SE"], "data": []}
with app.app_context():
g.user_session = UserSessionSimulator(None)
data = show_trait.ShowTrait(
cursor, user_id=None,
kw={
"trait_id": trait_id,
"dataset": dataset_name
}
)
attributes = data.js_data.get("attributes")
for id_ in attributes:
sample_data["headers"].append(attributes[id_].name)
for sample in data.js_data.get("sample_lists")[0]:
sample_data["data"].append(
[
sample.name,
sample.value or 'x',
sample.variance or 'x',
*[str(sample.extra_attributes.get(str(key), "x"))
for key in attributes],
])
return sample_data
def fetch_all_traits(species, group, type_, dataset):
with app.app_context():
g.user_session = UserSessionSimulator(None)
for result in SearchResultPage({
"species": species,
"group": group,
"type": type_,
"dataset": dataset,
"search_terms_or": "*",
}).trait_list:
yield result.get('name')
if __name__ == "__main__":
DATASET_NAME = "BXDPublish"
if not os.path.isdir(
BASE_DIR:=os.path.join(sys.argv[1],DATASET_NAME)
):
os.makedirs(BASE_DIR)
print("\n\n======================================\n\n")
print(f"Dumping Sampledata into {sys.argv[1]}:\n\n")
for trait in fetch_all_traits(
species="mouse",
group="BXD",
type_="Phenotypes",
dataset="BXDPublish",
):
# Dump all sample data into a given directory:
print(f"\033[FDumping: {DATASET_NAME}/{trait}")
with open(os.path.join(BASE_DIR, f"{trait}.json"), "w") as f:
json.dump(dump_sample_data(DATASET_NAME, trait), f)
print("DONE DUMPING!")
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