datacrossways_api/dbsetup.py at main · MaayanLab/datacrossways_api · GitHub

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from app import db, User, File, Collection, Role, UserRole, Policy, RolePolicy, PolicyCollections, PolicyFiles
import copy
import random

db.drop_all()
db.create_all()

user_1 = User(name='Alexander Lachmann',
                first_name="Alexander",
                last_name="Lachmann",
                affiliation="Mount Sinai Hospital",
                email="alexander.lachmann@gmail.com",
                orcid_id="0000-0002-1982-7652")

user_2 = User(name='Avi Ma\'ayan',
                first_name="Avi",
                last_name="Ma\'ayan",
                affiliation="Mount Sinai Hospital",
                email="avi.maayan@mssm.edu",
                orcid_id="0000-0002-1982-7653")

user_3 = User(name='Daniel Clarke',
                first_name="Daniel",
                last_name="Clarke",
                affiliation="Mount Sinai Hospital",
                email="u8sand@sand.com",
                orcid_id="0000-0002-1982-7654")

# needs to be created as a default for files if collection is not specified
root_collection = Collection(name="root", user=user_1)

file_1 = File(name="file_1.txt", user=user_1, collection=root_collection)
file_2 = File(name="file_2.txt", user=user_1, collection=root_collection)
file_3 = File(name="file_3.txt", user=user_1, collection=root_collection)

file_4 = File(name="file_4.txt", user=user_2, collection=root_collection)
file_5 = File(name="file_5.txt", user=user_2, collection=root_collection)
file_6 = File(name="file_6.txt", user=user_2, collection=root_collection)
file_7 = File(name="file_7.txt", user=user_2, collection=root_collection)

lyme_collection = Collection(name="lyme_data", user=user_3, parent=root_collection)

metadata = {
    "wow": "ok",
    "array": [1,3,4,5],
    "more": {
        "keeps_going": "nice",
        "present": True
    }
}

file_8 = File(name="file_8.txt", user=user_3, collection=lyme_collection, meta=metadata)
file_9 = File(name="file_9.txt", user=user_3, collection=lyme_collection, meta=metadata)
file_10 = File(name="file_10.txt", user=user_3, collection=lyme_collection, meta=copy.deepcopy(metadata))
file_11 = File(name="file_11.txt", user=user_3, collection=lyme_collection, meta=copy.deepcopy(metadata))

db.session.add_all([file_1, file_2, file_3, file_4, file_5, file_6, file_7, file_8, file_9, file_10, file_11])
db.session.commit()

uif = []
for r in range(10000):
    random.seed(r)
    metadata = {
        "id": r,
        "project": "p"+str(r%30),
        "array": [1,3,4,5],
        "creator": {
            "name": "c"+str(r%20),
            "present": True,
            "affiliation": "mssm"
        },
        "subject": {
            "id": r%500,
            "age": random.uniform(0, 100),
            "gender": random.choice(["male", "female"]),
            "ethnicity": random.choices(["Hispanic", "White", "Black or African American", "American Indian and Alaska Native", "Asian", "Native Hawaiian and Other Pacific Islander", "Other", "Multiracial"], weights=(30, 41, 28, 1, 14, 1, 14, 5), k=1)[0]
        },
        "experiment": {
            "group": random.choice(["control", "treatment"]),
        }
    }
    if r%2 == 0:
        metadata["extra"] = r
    f = File(name="file_"+str(r)+".txt", user=user_1, collection=lyme_collection, size=random.uniform(1000, 1000000), meta=copy.deepcopy(metadata))
    uif.append(f)

db.session.add_all(uif)
db.session.commit()

policy_1 = Policy(effect="allow", action="list")
policy_2 = Policy(effect="allow", action="read")
policy_3 = Policy(effect="allow", action="write")

policy_1.collections.append(root_collection)
policy_2.collections.append(root_collection)

admin_role = Role(name="admin")
user_1.roles.append(admin_role)

uploader_role = Role(name="uploader")
user_1.roles.append(uploader_role)

base_reader = Role(name="base_reader")
base_reader.policies.append(policy_1)
base_reader.policies.append(policy_2)

policy_3 = Policy(effect="allow", action="list")
policy_3.collections.append(root_collection)

policy = Policy(effect="allow", action="list")
policy.collections.append(lyme_collection)
lyme_lister = Role(name="lyme_lister")
lyme_lister.policies.append(policy_3)

policy = Policy(effect="allow", action="read")
policy.collections.append(lyme_collection)
lyme_reader = Role(name="lyme_reader")
lyme_reader.policies.append(policy)

user_2.roles.append(lyme_lister)
user_1.roles.append(lyme_lister)
user_1.roles.append(lyme_reader)

db.session.add_all([])

db.session.commit()


db.session.add(user_1)