diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 842469d1..3b9bd274 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
- id: isort
- repo: https://github.com/PyCQA/flake8
- rev: 3.9.2
+ rev: 7.0.0
hooks:
- id: flake8
args: ['--config=setup.cfg']
diff --git a/add_phenotype_inventory_input_example_data.py b/add_phenotype_inventory_input_example_data.py
new file mode 100644
index 00000000..427c6477
--- /dev/null
+++ b/add_phenotype_inventory_input_example_data.py
@@ -0,0 +1,50 @@
+# Temporary script to create some test data.
+# Run with: python manage.py shell < add_phenotype_inventory_input_example_data.py
+
+from anvil_consortium_manager.tests.factories import (
+ ManagedGroupFactory,
+ WorkspaceGroupSharingFactory,
+)
+
+from primed.cdsa.tests.factories import CDSAWorkspaceFactory
+from primed.dbgap.tests.factories import dbGaPWorkspaceFactory
+from primed.miscellaneous_workspaces.tests.factories import OpenAccessWorkspaceFactory
+from primed.primed_anvil.tests.factories import StudyFactory
+
+# Create a dbGaP workspace.
+fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study")
+workspace_dbgap = dbGaPWorkspaceFactory.create(
+ dbgap_study_accession__dbgap_phs=7,
+ dbgap_study_accession__studies=[fhs],
+ dbgap_version=33,
+ dbgap_participant_set=12,
+ dbgap_consent_code=1,
+ dbgap_consent_abbreviation="HMB",
+ workspace__name="DBGAP_FHS_v33_p12_HMB",
+)
+
+
+# Create a CDSA workspace.
+workspace_cdsa = CDSAWorkspaceFactory.create(
+ study__short_name="MESA",
+ workspace__name="CDSA_MESA_HMB",
+)
+
+# Create an open access workspace
+workspace_open_access = OpenAccessWorkspaceFactory.create(
+ workspace__name="OPEN_ACCESS_FHS",
+)
+workspace_open_access.studies.add(fhs)
+
+
+# Share workspaces with PRIMED_ALL
+primed_all = ManagedGroupFactory.create(name="PRIMED_ALL")
+WorkspaceGroupSharingFactory.create(
+ workspace=workspace_dbgap.workspace, group=primed_all
+)
+WorkspaceGroupSharingFactory.create(
+ workspace=workspace_cdsa.workspace, group=primed_all
+)
+WorkspaceGroupSharingFactory.create(
+ workspace=workspace_open_access.workspace, group=primed_all
+)
diff --git a/primed/primed_anvil/helpers.py b/primed/primed_anvil/helpers.py
index 39193ade..e0f6cacf 100644
--- a/primed/primed_anvil/helpers.py
+++ b/primed/primed_anvil/helpers.py
@@ -1,6 +1,9 @@
+from itertools import groupby
+
import pandas as pd
-from anvil_consortium_manager.models import WorkspaceGroupSharing
-from django.db.models import Exists, F, OuterRef, Value
+from anvil_consortium_manager.models import ManagedGroup, WorkspaceGroupSharing
+from django.db.models import CharField, Exists, F, OuterRef, Value
+from django.db.models.functions import Concat
from primed.cdsa.models import CDSAWorkspace
from primed.dbgap.models import dbGaPWorkspace
@@ -127,3 +130,96 @@ def get_summary_table_data():
# Convert to a list of dictionaries for passing to the django-tables2 table.
data = data.to_dict(orient="records")
return data
+
+
+def get_workspaces_for_phenotype_inventory():
+ """Get input to the primed-phenotype-inventory workflow.
+
+ This function generates the input for the "workspaces" field of the primed-phenotype-inventory workflow. Only
+ workspaces that have been shared with the consortium are included.
+ See dockstore link: https://dockstore.org/workflows/github.com/UW-GAC/primed-inventory-workflows/primed_phenotype_inventory:main?tab=info
+
+ The "workspaces" field has the format:
+ {
+ "billing-project-1/workspace-1": "study1, study2",
+ "billing-project-2/workspace-2": "study3",
+ ...
+ }
+ """ # noqa: E501
+
+ # primed-all group. We will need this to determine if the workspace is shared with PRIMED_ALL.
+ primed_all = ManagedGroup.objects.get(name="PRIMED_ALL")
+
+ dbgap_workspaces = (
+ dbGaPWorkspace.objects.filter(
+ # Just those that are shared with PRIMED_ALL.
+ workspace__workspacegroupsharing__group=primed_all,
+ )
+ .annotate(
+ workspace_name=Concat(
+ F("workspace__billing_project__name"),
+ Value("/"),
+ F("workspace__name"),
+ output_field=CharField(),
+ ),
+ study_names=F("dbgap_study_accession__studies__short_name"),
+ )
+ .values(
+ # "workspace",
+ # "workspace_billing_project",
+ "workspace_name",
+ "study_names",
+ )
+ )
+
+ cdsa_workspaces = (
+ CDSAWorkspace.objects.filter(
+ # Just those that are shared with PRIMED_ALL.
+ workspace__workspacegroupsharing__group=primed_all,
+ )
+ .annotate(
+ workspace_name=Concat(
+ F("workspace__billing_project__name"),
+ Value("/"),
+ F("workspace__name"),
+ output_field=CharField(),
+ ),
+ study_names=F("study__short_name"),
+ )
+ .values(
+ "workspace_name",
+ "study_names",
+ )
+ )
+
+ open_access_workspaces = (
+ OpenAccessWorkspace.objects.filter(
+ # Just those that are shared with PRIMED_ALL.
+ workspace__workspacegroupsharing__group=primed_all,
+ )
+ .annotate(
+ workspace_name=Concat(
+ F("workspace__billing_project__name"),
+ Value("/"),
+ F("workspace__name"),
+ output_field=CharField(),
+ ),
+ study_names=F("studies__short_name"),
+ )
+ .values(
+ "workspace_name",
+ "study_names",
+ )
+ )
+
+ # Combine all querysets and process into the expected output for the AnVIL workflow.
+ workspaces = dbgap_workspaces.union(cdsa_workspaces).union(open_access_workspaces)
+
+ json = {}
+ for key, group in groupby(workspaces, lambda x: x["workspace_name"]):
+ study_names = [x["study_names"] if x["study_names"] else "" for x in group]
+ if not study_names:
+ study_names = ""
+ json[key] = ", ".join(sorted(study_names))
+
+ return json
diff --git a/primed/primed_anvil/tests/test_helpers.py b/primed/primed_anvil/tests/test_helpers.py
index 78a20b57..a5bf54f1 100644
--- a/primed/primed_anvil/tests/test_helpers.py
+++ b/primed/primed_anvil/tests/test_helpers.py
@@ -1,10 +1,16 @@
"""Tests of helper functions in the `primed_anvil` app."""
-from anvil_consortium_manager.tests.factories import WorkspaceGroupSharingFactory
+from anvil_consortium_manager.tests.factories import (
+ ManagedGroupFactory,
+ WorkspaceGroupSharingFactory,
+)
from django.test import TestCase
from primed.cdsa.tests.factories import CDSAWorkspaceFactory
-from primed.dbgap.tests.factories import dbGaPWorkspaceFactory
+from primed.dbgap.tests.factories import (
+ dbGaPStudyAccessionFactory,
+ dbGaPWorkspaceFactory,
+)
from primed.miscellaneous_workspaces.tests.factories import OpenAccessWorkspaceFactory
from primed.primed_anvil.tests.factories import AvailableDataFactory, StudyFactory
@@ -544,3 +550,290 @@ def test_one_cdsa_workspace_one_open_access_workspace_different_available_data(
},
res,
)
+
+
+class GetWorkspacesForPhenotypeInventoryTest(TestCase):
+ """Tests for the helpers.get_workspaces_for_phenotype_inventory method."""
+
+ def setUp(self):
+ """Set up the test case."""
+ super().setUp()
+ # Create the PRIMED_ALL group.
+ self.primed_all_group = ManagedGroupFactory.create(name="PRIMED_ALL")
+
+ def test_no_workspaces(self):
+ """get_workspaces_for_phenotype_inventory with no workspaces."""
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(res, {})
+
+ def test_one_dbgap_workspace_not_shared(self):
+ """get_workspaces_for_phenotype_inventory with one dbGaP workspace."""
+ dbGaPWorkspaceFactory.create()
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(res, {})
+
+ def test_one_dbgap_workspace_shared_one_study(self):
+ """get_workspaces_for_phenotype_inventory with one dbGaP workspace."""
+ study = StudyFactory.create(short_name="TEST")
+ workspace = dbGaPWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp",
+ workspace__name="test-ws",
+ dbgap_study_accession__studies=[study],
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 1)
+ self.assertIn("test-bp/test-ws", res)
+ self.assertEqual(res["test-bp/test-ws"], "TEST")
+
+ def test_one_dbgap_workspace_shared_two_studies(self):
+ """get_workspaces_for_phenotype_inventory with one dbGaP workspace."""
+ study_1 = StudyFactory.create(short_name="TEST_2")
+ study_2 = StudyFactory.create(short_name="TEST_1")
+ study_accession = dbGaPStudyAccessionFactory.create(studies=[study_1, study_2])
+ workspace = dbGaPWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp",
+ workspace__name="test-ws",
+ dbgap_study_accession=study_accession,
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 1)
+ self.assertIn("test-bp/test-ws", res)
+ self.assertEqual(res["test-bp/test-ws"], "TEST_1, TEST_2")
+
+ def test_two_dbgap_workspaces(self):
+ """get_workspaces_for_phenotype_inventory with two dbGaP workspaces."""
+ study_1 = StudyFactory.create(short_name="TEST 1")
+ workspace_1 = dbGaPWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-1",
+ workspace__name="test-ws-1",
+ dbgap_study_accession__studies=[study_1],
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace_1.workspace, group=self.primed_all_group
+ )
+ study_2 = StudyFactory.create(short_name="TEST 2")
+ workspace_2 = dbGaPWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-2",
+ workspace__name="test-ws-2",
+ dbgap_study_accession__studies=[study_2],
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace_2.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 2)
+ self.assertIn("test-bp-1/test-ws-1", res)
+ self.assertEqual(res["test-bp-1/test-ws-1"], "TEST 1")
+ self.assertIn("test-bp-2/test-ws-2", res)
+ self.assertEqual(res["test-bp-2/test-ws-2"], "TEST 2")
+
+ def test_one_cdsa_workspace_not_shared(self):
+ """get_workspaces_for_phenotype_inventory with one CDSA workspace."""
+ CDSAWorkspaceFactory.create()
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(res, {})
+
+ def test_one_cdsa_workspace_shared_one_study(self):
+ """get_workspaces_for_phenotype_inventory with one CDSA workspace."""
+ study = StudyFactory.create(short_name="TEST")
+ workspace = CDSAWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp",
+ workspace__name="test-ws",
+ study=study,
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 1)
+ self.assertIn("test-bp/test-ws", res)
+ self.assertEqual(res["test-bp/test-ws"], "TEST")
+
+ def test_two_cdsa_workspaces(self):
+ """get_workspaces_for_phenotype_inventory with two CDSA workspaces."""
+ study_1 = StudyFactory.create(short_name="TEST 1")
+ workspace_1 = CDSAWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-1",
+ workspace__name="test-ws-1",
+ study=study_1,
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace_1.workspace, group=self.primed_all_group
+ )
+ study_2 = StudyFactory.create(short_name="TEST 2")
+ workspace_2 = CDSAWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-2",
+ workspace__name="test-ws-2",
+ study=study_2,
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace_2.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 2)
+ self.assertIn("test-bp-1/test-ws-1", res)
+ self.assertEqual(res["test-bp-1/test-ws-1"], "TEST 1")
+ self.assertIn("test-bp-2/test-ws-2", res)
+ self.assertEqual(res["test-bp-2/test-ws-2"], "TEST 2")
+
+ def test_one_open_access_workspace_not_shared(self):
+ """get_workspaces_for_phenotype_inventory with one dbGaP workspace."""
+ OpenAccessWorkspaceFactory.create()
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(res, {})
+
+ def test_one_open_access_workspace_shared_no_study(self):
+ """get_workspaces_for_phenotype_inventory with one Open access workspace."""
+ workspace = OpenAccessWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp",
+ workspace__name="test-ws",
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 1)
+ self.assertIn("test-bp/test-ws", res)
+ self.assertEqual(res["test-bp/test-ws"], "")
+
+ def test_one_open_access_workspace_shared_one_study(self):
+ """get_workspaces_for_phenotype_inventory with one Open access workspace."""
+ study = StudyFactory.create(short_name="TEST")
+ workspace = OpenAccessWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp",
+ workspace__name="test-ws",
+ )
+ workspace.studies.add(study)
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 1)
+ self.assertIn("test-bp/test-ws", res)
+ self.assertEqual(res["test-bp/test-ws"], "TEST")
+
+ def test_one_open_access_workspace_shared_two_studies(self):
+ """get_workspaces_for_phenotype_inventory with one Open access workspace."""
+ study_1 = StudyFactory.create(short_name="TEST_2")
+ study_2 = StudyFactory.create(short_name="TEST_1")
+ workspace = OpenAccessWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp",
+ workspace__name="test-ws",
+ )
+ workspace.studies.add(study_1, study_2)
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 1)
+ self.assertIn("test-bp/test-ws", res)
+ self.assertEqual(res["test-bp/test-ws"], "TEST_1, TEST_2")
+
+ def test_two_open_access_workspaces(self):
+ """get_workspaces_for_phenotype_inventory with two Open access workspace."""
+ workspace_1 = OpenAccessWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-1",
+ workspace__name="test-ws-1",
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace_1.workspace, group=self.primed_all_group
+ )
+ study_2 = StudyFactory.create(short_name="TEST 2")
+ workspace_2 = OpenAccessWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-2",
+ workspace__name="test-ws-2",
+ )
+ workspace_2.studies.add(study_2)
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace_2.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 2)
+ self.assertIn("test-bp-1/test-ws-1", res)
+ self.assertEqual(res["test-bp-1/test-ws-1"], "")
+ self.assertIn("test-bp-2/test-ws-2", res)
+ self.assertEqual(res["test-bp-2/test-ws-2"], "TEST 2")
+
+ def test_multiple_workspace_types_same_study(self):
+ study = StudyFactory.create(short_name="TEST")
+ # dbgap
+ workspace = dbGaPWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-dbgap",
+ workspace__name="test-ws-dbgap",
+ dbgap_study_accession__studies=[study],
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ # CDSA
+ workspace = CDSAWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-cdsa",
+ workspace__name="test-ws-cdsa",
+ study=study,
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ # Open access
+ workspace = OpenAccessWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-open",
+ workspace__name="test-ws-open",
+ )
+ workspace.studies.add(study)
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 3)
+ self.assertIn("test-bp-dbgap/test-ws-dbgap", res)
+ self.assertEqual(res["test-bp-dbgap/test-ws-dbgap"], "TEST")
+ self.assertIn("test-bp-cdsa/test-ws-cdsa", res)
+ self.assertEqual(res["test-bp-cdsa/test-ws-cdsa"], "TEST")
+ self.assertIn("test-bp-open/test-ws-open", res)
+ self.assertEqual(res["test-bp-open/test-ws-open"], "TEST")
+
+ def test_multiple_workspace_types_separate_studies(self):
+ study_1 = StudyFactory.create(short_name="TEST 1")
+ # dbgap
+ workspace = dbGaPWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-dbgap",
+ workspace__name="test-ws-dbgap",
+ dbgap_study_accession__studies=[study_1],
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ # CDSA
+ study_2 = StudyFactory.create(short_name="TEST 2")
+ workspace = CDSAWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-cdsa",
+ workspace__name="test-ws-cdsa",
+ study=study_2,
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ # Open access
+ study_3 = StudyFactory.create(short_name="TEST 3")
+ workspace = OpenAccessWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp-open",
+ workspace__name="test-ws-open",
+ )
+ workspace.studies.add(study_3)
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all_group
+ )
+ res = helpers.get_workspaces_for_phenotype_inventory()
+ self.assertEqual(len(res), 3)
+ self.assertIn("test-bp-dbgap/test-ws-dbgap", res)
+ self.assertEqual(res["test-bp-dbgap/test-ws-dbgap"], "TEST 1")
+ self.assertIn("test-bp-cdsa/test-ws-cdsa", res)
+ self.assertEqual(res["test-bp-cdsa/test-ws-cdsa"], "TEST 2")
+ self.assertIn("test-bp-open/test-ws-open", res)
+ self.assertEqual(res["test-bp-open/test-ws-open"], "TEST 3")
diff --git a/primed/primed_anvil/tests/test_views.py b/primed/primed_anvil/tests/test_views.py
index 9a95ea11..b800b6df 100644
--- a/primed/primed_anvil/tests/test_views.py
+++ b/primed/primed_anvil/tests/test_views.py
@@ -1,7 +1,11 @@
import json
from anvil_consortium_manager import models as acm_models
-from anvil_consortium_manager.tests.factories import AccountFactory
+from anvil_consortium_manager.tests.factories import (
+ AccountFactory,
+ ManagedGroupFactory,
+ WorkspaceGroupSharingFactory,
+)
from anvil_consortium_manager.views import AccountList
from constance.test import override_config
from django.conf import settings
@@ -1267,3 +1271,81 @@ def test_includes_cdsa_workspaces(self):
response = self.client.get(self.get_url())
self.assertIn("summary_table", response.context_data)
self.assertEqual(len(response.context_data["summary_table"].rows), 1)
+
+
+class PhenotypeInventoryInputsViewTest(TestCase):
+ """Tests for the PhenotypeInventoryInputsView view."""
+
+ def setUp(self):
+ """Set up test class."""
+ self.factory = RequestFactory()
+ # Create a user with both view and edit permission.
+ self.user = User.objects.create_user(username="test", password="test")
+ self.user.user_permissions.add(
+ Permission.objects.get(
+ codename=acm_models.AnVILProjectManagerAccess.STAFF_VIEW_PERMISSION_CODENAME
+ )
+ )
+ self.primed_all = ManagedGroupFactory.create(name="PRIMED_ALL")
+
+ def get_url(self, *args):
+ """Get the url for the view being tested."""
+ return reverse("primed_anvil:utilities:phenotype_inventory_inputs", args=args)
+
+ def get_view(self):
+ """Return the view being tested."""
+ return views.PhenotypeInventoryInputsView.as_view()
+
+ def test_view_redirect_not_logged_in(self):
+ "View redirects to login view when user is not logged in."
+ # Need a client for redirects.
+ response = self.client.get(self.get_url())
+ self.assertRedirects(
+ response, resolve_url(settings.LOGIN_URL) + "?next=" + self.get_url()
+ )
+
+ def test_status_code_with_authenticated_user(self):
+ """Redirects to login view when user has no perms."""
+ user_no_perms = User.objects.create_user(
+ username="test-none", password="test-none"
+ )
+ request = self.factory.get(self.get_url())
+ request.user = user_no_perms
+ with self.assertRaises(PermissionDenied):
+ self.get_view()(request)
+
+ def test_status_code_with_view_user(self):
+ """Redirects to login view when user has view perm."""
+ user = User.objects.create_user(username="test-none", password="test-none")
+ user.user_permissions.add(
+ Permission.objects.get(
+ codename=acm_models.AnVILProjectManagerAccess.VIEW_PERMISSION_CODENAME
+ )
+ )
+ request = self.factory.get(self.get_url())
+ request.user = user
+ with self.assertRaises(PermissionDenied):
+ self.get_view()(request)
+
+ def test_context_workspaces_input_no_workspaces(self):
+ """workspaces_input exists in the context and is correct with no workspaces."""
+ self.client.force_login(self.user)
+ response = self.client.get(self.get_url())
+ self.assertIn("workspaces_input", response.context_data)
+ self.assertEqual(response.context_data["workspaces_input"], "{}")
+
+ def test_context_workspaces_input_one_workspace(self):
+ """workspaces_input exists in the context and is correct with one shared workspace."""
+ workspace = OpenAccessWorkspaceFactory.create(
+ workspace__billing_project__name="test-bp", workspace__name="test-ws"
+ )
+ WorkspaceGroupSharingFactory.create(
+ workspace=workspace.workspace, group=self.primed_all
+ )
+ self.client.force_login(self.user)
+ response = self.client.get(self.get_url())
+ self.assertIn("workspaces_input", response.context_data)
+ self.assertEqual(
+ response.context_data["workspaces_input"],
+ """{\n "test-bp/test-ws": ""\n}""",
+ )
diff --git a/primed/primed_anvil/urls.py b/primed/primed_anvil/urls.py
index 909ad7fb..81557dcf 100644
--- a/primed/primed_anvil/urls.py
+++ b/primed/primed_anvil/urls.py
@@ -37,9 +37,21 @@
"summaries",
)
+utilities_patterns = (
+ [
+ path(
+ "phenotype_inventory_inputs/",
+ views.PhenotypeInventoryInputsView.as_view(),
+ name="phenotype_inventory_inputs",
+ ),
+ ],
+ "utilities",
+)
+
urlpatterns = [
path("studies/", include(study_patterns)),
path("study_sites/", include(study_site_patterns)),
path("available_data/", include(available_data_patterns)),
path("summaries/", include(summary_patterns)),
+ path("utilities/", include(utilities_patterns)),
]
diff --git a/primed/primed_anvil/views.py b/primed/primed_anvil/views.py
index c89ab3cb..f85e787b 100644
--- a/primed/primed_anvil/views.py
+++ b/primed/primed_anvil/views.py
@@ -1,3 +1,5 @@
+import json
+
from anvil_consortium_manager.auth import (
AnVILConsortiumManagerStaffEditRequired,
AnVILConsortiumManagerStaffViewRequired,
@@ -183,3 +185,17 @@ def get_context_data(self, **kwargs):
table_data = helpers.get_summary_table_data()
context["summary_table"] = tables.DataSummaryTable(table_data)
return context
+
+
+class PhenotypeInventoryInputsView(
+ AnVILConsortiumManagerStaffViewRequired, TemplateView
+):
+
+ template_name = "primed_anvil/phenotype_inventory_inputs.html"
+
+ def get_context_data(self, **kwargs):
+ context = super().get_context_data(**kwargs)
+ context["workspaces_input"] = json.dumps(
+ helpers.get_workspaces_for_phenotype_inventory(), indent=2
+ )
+ return context
diff --git a/primed/templates/primed_anvil/phenotype_inventory_inputs.html b/primed/templates/primed_anvil/phenotype_inventory_inputs.html
new file mode 100644
index 00000000..7dc372ce
--- /dev/null
+++ b/primed/templates/primed_anvil/phenotype_inventory_inputs.html
@@ -0,0 +1,57 @@
+{% extends 'base.html' %}
+{% load render_table from django_tables2 %}
+
+{% block extra_navbar %}
+ {% include 'anvil_consortium_manager/navbar.html' %}
+{% endblock %}
+
+{% block content %}
+
+
Phenotype inventory workflow
+
+
+ This page creates the input for the "workspaces" field in the
+ PRIMED phenotype inventory workflow.
+ Copy the text in the box below and paste it into the "workspaces" field when running the workflow on AnVIL.
+