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import json
# 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": "10007",
"dataset": "BXDPublish",
}
)
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')
# Dump all traits from a given dataset
for trait in fetch_all_traits(
species="mouse",
group="BXD",
type_="Phenotypes",
dataset="BXDPublish",
):
print(json.dumps(dump_sample_data("BXDPublish", trait)))
break # Just do this once!
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