add_cdsa_example_data.py

# Temporary script to create some test data.
# Run with: python manage.py shell < add_cdsa_example_data.py

from anvil_consortium_manager.tests.factories import (
    AccountFactory,
    GroupAccountMembershipFactory,
    GroupGroupMembershipFactory,
    ManagedGroupFactory,
)
from django.conf import settings
from django.core.management import call_command

from primed.cdsa.tests import factories
from primed.duo.models import DataUseModifier, DataUsePermission
from primed.primed_anvil.models import Study, StudySite
from primed.primed_anvil.tests.factories import StudyFactory, StudySiteFactory
from primed.users.models import User
from primed.users.tests.factories import UserFactory

# Load duos
call_command("load_duo")

# create the CDSA auth group
cdsa_group = ManagedGroupFactory.create(name=settings.ANVIL_CDSA_GROUP_NAME)
# Add PRIMED ADMINS group
cc_admins_group = ManagedGroupFactory.create(name=settings.ANVIL_CC_ADMINS_GROUP_NAME)

# Create major versions
major_version = factories.AgreementMajorVersionFactory.create(version=1)

# Create some agreement versions
v10 = factories.AgreementVersionFactory.create(major_version=major_version, minor_version=0)
v11 = factories.AgreementVersionFactory.create(major_version=major_version, minor_version=1)

# Create a couple signed CDSAs.
dup = DataUsePermission.objects.get(abbreviation="GRU")
dum = DataUseModifier.objects.get(abbreviation="NPU")

# Create some study sites.
try:
    cc = StudySite.objects.get(short_name="CC")
except StudySite.DoesNotExist:
    cc = StudySiteFactory.create(short_name="CC", full_name="Coordinating Center")
try:
    cardinal = StudySite.objects.get(short_name="CARDINAL")
except StudySite.DoesNotExist:
    cardinal = StudySiteFactory.create(short_name="CARDINAL", full_name="CARDINAL")

# Create some studies.
try:
    amish = Study.objects.get(short_name="Amish")
except Study.DoesNotExist:
    amish = StudyFactory.create(short_name="Amish", full_name="Amish")
try:
    mesa = Study.objects.get(short_name="MESA")
except Study.DoesNotExist:
    mesa = StudyFactory.create(short_name="MESA", full_name="MESA")
try:
    aric = Study.objects.get(short_name="ARIC")
except Study.DoesNotExist:
    aric = Study.objects.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities")

# Create some CDSAs
cdsa_1001 = factories.MemberAgreementFactory.create(
    signed_agreement__cc_id=1001,
    signed_agreement__representative=UserFactory.create(name="Ken Rice"),
    signed_agreement__signing_institution="UW",
    signed_agreement__representative_role="Contact PI",
    is_primary=True,
    signed_agreement__version=v10,
    study_site=cc,
)
cdsa_1001.signed_agreement.representative.study_sites.add(cc)
GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1001.signed_agreement.anvil_access_group)

cdsa_1002 = factories.MemberAgreementFactory.create(
    signed_agreement__cc_id=1002,
    signed_agreement__representative=UserFactory.create(name="Sally Adebamowo"),
    signed_agreement__signing_institution="UM",
    signed_agreement__representative_role="Contact PI",
    is_primary=True,
    signed_agreement__version=v10,
    study_site=cardinal,
)
cdsa_1002.signed_agreement.representative.study_sites.add(cardinal)
GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1002.signed_agreement.anvil_access_group)

cdsa_1003 = factories.MemberAgreementFactory.create(
    signed_agreement__cc_id=1003,
    signed_agreement__representative=UserFactory.create(name="Bamidele Tayo"),
    signed_agreement__signing_institution="Loyola",
    signed_agreement__representative_role="Co-PI",
    is_primary=False,
    signed_agreement__version=v10,
    study_site=cardinal,
)
GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1003.signed_agreement.anvil_access_group)

cdsa_1004 = factories.MemberAgreementFactory.create(
    signed_agreement__cc_id=1004,
    signed_agreement__representative=UserFactory.create(name="Brackie Mitchell"),
    signed_agreement__signing_institution="UM",
    signed_agreement__representative_role="Co-I",
    is_primary=False,
    signed_agreement__version=v11,
    study_site=cardinal,
)
GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1004.signed_agreement.anvil_access_group)

cdsa_1005 = factories.DataAffiliateAgreementFactory.create(
    signed_agreement__cc_id=1005,
    signed_agreement__representative=User.objects.get(name="Brackie Mitchell"),
    signed_agreement__signing_institution="UMaryland",
    signed_agreement__representative_role="Study PI",
    study=amish,
    signed_agreement__version=v10,
)
GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1005.signed_agreement.anvil_access_group)

cdsa_1006 = factories.DataAffiliateAgreementFactory.create(
    signed_agreement__cc_id=1006,
    signed_agreement__representative=UserFactory.create(name="Robyn"),
    signed_agreement__representative_role="DCC PI",
    signed_agreement__signing_institution="UW",
    study=mesa,
    signed_agreement__version=v10,
    additional_limitations="This data can only be used for testing the app.",
    requires_study_review=True,
)
GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1006.signed_agreement.anvil_access_group)

cdsa_1007 = factories.DataAffiliateAgreementFactory.create(
    signed_agreement__cc_id=1007,
    signed_agreement__representative=UserFactory.create(name="Wendy"),
    signed_agreement__signing_institution="JHU",
    signed_agreement__representative_role="Field Center PI",
    is_primary=False,
    study=mesa,
    signed_agreement__version=v10,
)
GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1007.signed_agreement.anvil_access_group)

cdsa_1008 = factories.DataAffiliateAgreementFactory.create(
    signed_agreement__cc_id=1008,
    signed_agreement__representative=UserFactory.create(name="Jerry"),
    signed_agreement__signing_institution="Lundquist",
    signed_agreement__representative_role="Analysis Center PI",
    is_primary=False,
    study=mesa,
    signed_agreement__version=v10,
)
GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1008.signed_agreement.anvil_access_group)

cdsa_1009 = factories.NonDataAffiliateAgreementFactory.create(
    signed_agreement__cc_id=1009,
    signed_agreement__representative=UserFactory.create(name="ExpertA"),
    signed_agreement__signing_institution="UABC",
    affiliation="CenterXYZ",
    signed_agreement__representative_role="Contact PI",
    signed_agreement__version=v10,
)
# DO not add to cdsa group to demonstrate audit
# GroupGroupMembershipFactory.create(
#     parent_group=cdsa_group, child_group=cdsa_1009.signed_agreement.anvil_access_group
# )


# Add some users to the CDSA groups.
users = UserFactory.create_batch(12)
cdsa_1001.signed_agreement.accessors.add(users[0])
GroupAccountMembershipFactory.create(
    group=cdsa_1001.signed_agreement.anvil_access_group,
    account__user=users[0],
)
# # Do not add as an accessor so we can check auditing.
# cdsa_1001.signed_agreement.accessors.add(users[1])
GroupAccountMembershipFactory.create(
    group=cdsa_1001.signed_agreement.anvil_access_group,
    account__user=users[1],
)
cdsa_1001.signed_agreement.accessors.add(users[2])
AccountFactory.create(user=users[2])
# # Do not create the GroupAccountMembership so we can check auditing.
# GroupAccountMembershipFactory.create(
#     group=cdsa_1001.signed_agreement.anvil_access_group,
#     account__user=users[2],
# )
cdsa_1002.signed_agreement.accessors.add(users[3])
GroupAccountMembershipFactory.create(
    group=cdsa_1002.signed_agreement.anvil_access_group,
    account__user=users[3],
)
cdsa_1002.signed_agreement.accessors.add(users[4])
GroupAccountMembershipFactory.create(
    group=cdsa_1002.signed_agreement.anvil_access_group,
    account__user=users[4],
)
cdsa_1003.signed_agreement.accessors.add(users[5])
GroupAccountMembershipFactory.create(
    group=cdsa_1003.signed_agreement.anvil_access_group,
    account__user=users[5],
)
cdsa_1005.signed_agreement.accessors.add(users[6])
GroupAccountMembershipFactory.create(
    group=cdsa_1005.signed_agreement.anvil_access_group,
    account__user=users[6],
)
cdsa_1005.signed_agreement.accessors.add(users[7])
GroupAccountMembershipFactory.create(
    group=cdsa_1005.signed_agreement.anvil_access_group,
    account__user=users[7],
)
cdsa_1006.signed_agreement.accessors.add(users[8])
GroupAccountMembershipFactory.create(
    group=cdsa_1006.signed_agreement.anvil_access_group,
    account__user=users[8],
)
cdsa_1006.signed_agreement.accessors.add(users[9])
GroupAccountMembershipFactory.create(
    group=cdsa_1006.signed_agreement.anvil_access_group,
    account__user=users[9],
)
# Add uploaders.
cdsa_1006.uploaders.add(users[10])
AccountFactory.create(user=users[10])
cdsa_1006.uploaders.add(users[11])

cdsa_workspace_1 = factories.CDSAWorkspaceFactory.create(
    workspace__billing_project__name="demo-primed-cdsa",
    workspace__name="DEMO_PRIMED_CDSA_MESA_1",
    study=mesa,
    data_use_permission=dup,
)
GroupGroupMembershipFactory.create(
    parent_group=cdsa_workspace_1.workspace.authorization_domains.first(),
    child_group=cdsa_group,
)


# Create a second workspace.
cdsa_workspace_2 = factories.CDSAWorkspaceFactory.create(
    workspace__billing_project__name="demo-primed-cdsa",
    workspace__name="DEMO_PRIMED_CDSA_MESA_2",
    study=mesa,
    data_use_permission=dup,
    additional_limitations="Additional limitations for workspace.",
)
cdsa_workspace_2.data_use_modifiers.add(dum)


# Add a workspace with no primary cdsa.
cdsa_workspace_3 = factories.CDSAWorkspaceFactory.create(
    workspace__billing_project__name="demo-primed-cdsa",
    workspace__name="DEMO_PRIMED_CDSA_ARIC_1",
    study=aric,
    data_use_permission=dup,
)