Rename phenotype inventory to just "inventory"

Since we now have a genotype inventory, it better fits the use case.

add_phenotype_inventory_input_example_data.py → add_inventory_input_example_data.py

@@ -1,5 +1,5 @@
 # Temporary script to create some test data.
-# Run with: python manage.py shell < add_phenotype_inventory_input_example_data.py
+# Run with: python manage.py shell < add_inventory_input_example_data.py
 
 from anvil_consortium_manager.tests.factories import (
     ManagedGroupFactory,

primed/primed_anvil/helpers.py

@@ -130,12 +130,12 @@ def get_summary_table_data():
     return data
 
 
-def get_workspaces_for_phenotype_inventory():
+def get_workspaces_for_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
+    See dockstore link: https://dockstore.org/workflows/github.com/UW-GAC/primed-inventory-workflows/primed_inventory:main?tab=info
 
     The "workspaces" field has the format:
     {

primed/primed_anvil/tests/test_helpers.py

@@ -541,7 +541,7 @@ def test_one_cdsa_workspace_one_open_access_workspace_different_available_data(
 
 
 class GetWorkspacesForPhenotypeInventoryTest(TestCase):
-    """Tests for the helpers.get_workspaces_for_phenotype_inventory method."""
+    """Tests for the helpers.get_workspaces_for_inventory method."""
 
     def setUp(self):
         """Set up the test case."""
@@ -550,32 +550,32 @@ def setUp(self):
         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()
+        """get_workspaces_for_inventory with no workspaces."""
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(res, {})
 
     def test_one_dbgap_workspace_not_shared(self):
-        """get_workspaces_for_phenotype_inventory with one dbGaP workspace."""
+        """get_workspaces_for_inventory with one dbGaP workspace."""
         dbGaPWorkspaceFactory.create()
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(res, {})
 
     def test_one_dbgap_workspace_shared_one_study(self):
-        """get_workspaces_for_phenotype_inventory with one dbGaP workspace."""
+        """get_workspaces_for_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()
+        res = helpers.get_workspaces_for_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."""
+        """get_workspaces_for_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])
@@ -585,13 +585,13 @@ def test_one_dbgap_workspace_shared_two_studies(self):
             dbgap_study_accession=study_accession,
         )
         WorkspaceGroupSharingFactory.create(workspace=workspace.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_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."""
+        """get_workspaces_for_inventory with two dbGaP workspaces."""
         study_1 = StudyFactory.create(short_name="TEST 1")
         workspace_1 = dbGaPWorkspaceFactory.create(
             workspace__billing_project__name="test-bp-1",
@@ -606,35 +606,35 @@ def test_two_dbgap_workspaces(self):
             dbgap_study_accession__studies=[study_2],
         )
         WorkspaceGroupSharingFactory.create(workspace=workspace_2.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_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."""
+        """get_workspaces_for_inventory with one CDSA workspace."""
         CDSAWorkspaceFactory.create()
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(res, {})
 
     def test_one_cdsa_workspace_shared_one_study(self):
-        """get_workspaces_for_phenotype_inventory with one CDSA workspace."""
+        """get_workspaces_for_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()
+        res = helpers.get_workspaces_for_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."""
+        """get_workspaces_for_inventory with two CDSA workspaces."""
         study_1 = StudyFactory.create(short_name="TEST 1")
         workspace_1 = CDSAWorkspaceFactory.create(
             workspace__billing_project__name="test-bp-1",
@@ -649,47 +649,47 @@ def test_two_cdsa_workspaces(self):
             study=study_2,
         )
         WorkspaceGroupSharingFactory.create(workspace=workspace_2.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_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."""
+        """get_workspaces_for_inventory with one dbGaP workspace."""
         OpenAccessWorkspaceFactory.create()
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(res, {})
 
     def test_one_open_access_workspace_shared_no_study(self):
-        """get_workspaces_for_phenotype_inventory with one Open access workspace."""
+        """get_workspaces_for_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()
+        res = helpers.get_workspaces_for_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."""
+        """get_workspaces_for_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()
+        res = helpers.get_workspaces_for_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."""
+        """get_workspaces_for_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(
@@ -698,13 +698,13 @@ def test_one_open_access_workspace_shared_two_studies(self):
         )
         workspace.studies.add(study_1, study_2)
         WorkspaceGroupSharingFactory.create(workspace=workspace.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_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."""
+        """get_workspaces_for_inventory with two Open access workspace."""
         workspace_1 = OpenAccessWorkspaceFactory.create(
             workspace__billing_project__name="test-bp-1",
             workspace__name="test-ws-1",
@@ -717,7 +717,7 @@ def test_two_open_access_workspaces(self):
         )
         workspace_2.studies.add(study_2)
         WorkspaceGroupSharingFactory.create(workspace=workspace_2.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(len(res), 2)
         self.assertIn("test-bp-1/test-ws-1", res)
         self.assertEqual(res["test-bp-1/test-ws-1"], "")
@@ -747,7 +747,7 @@ def test_multiple_workspace_types_same_study(self):
         )
         workspace.studies.add(study)
         WorkspaceGroupSharingFactory.create(workspace=workspace.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_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")
@@ -781,7 +781,7 @@ def test_multiple_workspace_types_separate_studies(self):
         )
         workspace.studies.add(study_3)
         WorkspaceGroupSharingFactory.create(workspace=workspace.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_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")
@@ -850,7 +850,7 @@ def test_non_consecutive_grouping(self):
             dbgap_study_accession=study_accession_1,
         )
         WorkspaceGroupSharingFactory.create(workspace=workspace_1_d.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(len(res), 8)
         self.assertEqual(res["test-b/test-a-b_c1"], "TEST_1, TEST_2")
         self.assertEqual(res["test-b/test-a-b_c2"], "TEST_1, TEST_2")
@@ -878,7 +878,7 @@ def test_order_dbgap(self):
             workspace__name="test-ws-2",
         )
         WorkspaceGroupSharingFactory.create(workspace=workspace_3.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(len(res), 3)
         self.assertEqual(list(res)[0], "test-bp-1/test-ws-2")
         self.assertEqual(list(res)[1], "test-bp-2/test-ws-1")
@@ -901,7 +901,7 @@ def test_order_cdsa(self):
             workspace__name="test-ws-2",
         )
         WorkspaceGroupSharingFactory.create(workspace=workspace_3.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(len(res), 3)
         self.assertEqual(list(res)[0], "test-bp-1/test-ws-2")
         self.assertEqual(list(res)[1], "test-bp-2/test-ws-1")
@@ -924,7 +924,7 @@ def test_order_open_access(self):
             workspace__name="test-ws-2",
         )
         WorkspaceGroupSharingFactory.create(workspace=workspace_3.workspace, group=self.primed_all_group)
-        res = helpers.get_workspaces_for_phenotype_inventory()
+        res = helpers.get_workspaces_for_inventory()
         self.assertEqual(len(res), 3)
         self.assertEqual(list(res)[0], "test-bp-1/test-ws-2")
         self.assertEqual(list(res)[1], "test-bp-2/test-ws-1")

primed/primed_anvil/tests/test_views.py

@@ -1247,8 +1247,8 @@ def test_includes_cdsa_workspaces(self):
         self.assertEqual(len(response.context_data["summary_table"].rows), 1)
 
 
-class PhenotypeInventoryInputsViewTest(TestCase):
-    """Tests for the PhenotypeInventoryInputsView view."""
+class InventoryInputsViewTest(TestCase):
+    """Tests for the InventoryInputsView view."""
 
     def setUp(self):
         """Set up test class."""
@@ -1262,11 +1262,11 @@ def setUp(self):
 
     def get_url(self, *args):
         """Get the url for the view being tested."""
-        return reverse("primed_anvil:utilities:phenotype_inventory_inputs", args=args)
+        return reverse("primed_anvil:utilities:inventory_inputs", args=args)
 
     def get_view(self):
         """Return the view being tested."""
-        return views.PhenotypeInventoryInputsView.as_view()
+        return views.InventoryInputsView.as_view()
 
     def test_view_redirect_not_logged_in(self):
         "View redirects to login view when user is not logged in."

primed/primed_anvil/urls.py

@@ -40,9 +40,9 @@
 utilities_patterns = (
     [
         path(
-            "phenotype_inventory_inputs/",
-            views.PhenotypeInventoryInputsView.as_view(),
-            name="phenotype_inventory_inputs",
+            "inventory_inputs/",
+            views.InventoryInputsView.as_view(),
+            name="inventory_inputs",
         ),
     ],
     "utilities",

primed/primed_anvil/views.py

@@ -180,10 +180,10 @@ def get_context_data(self, **kwargs):
         return context
 
 
-class PhenotypeInventoryInputsView(AnVILConsortiumManagerStaffViewRequired, TemplateView):
-    template_name = "primed_anvil/phenotype_inventory_inputs.html"
+class InventoryInputsView(AnVILConsortiumManagerStaffViewRequired, TemplateView):
+    template_name = "primed_anvil/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)
+        context["workspaces_input"] = json.dumps(helpers.get_workspaces_for_inventory(), indent=2)
         return context

primed/templates/anvil_consortium_manager/navbar.html

@@ -36,7 +36,7 @@
 
       <li><hr class="dropdown-divider"></li>
       <li>
-        <a class="dropdown-item" href="{% url 'primed_anvil:utilities:phenotype_inventory_inputs' %}">Phenotype inventory</a>
+        <a class="dropdown-item" href="{% url 'primed_anvil:utilities:inventory_inputs' %}">Inventory inputs</a>
       </li>
 
       <li><hr class="dropdown-divider"></li>

primed/templates/primed_anvil/phenotype_inventory_inputs.html → primed/templates/primed_anvil/inventory_inputs.html

@@ -11,7 +11,7 @@ <h2>Phenotype inventory workflow</h2>
 
 <p>
   This page creates the input for the "workspaces" field in the
-  <a href="https://dockstore.org/workflows/github.com/UW-GAC/primed-inventory-workflows/primed_phenotype_inventory:main?tab=info">PRIMED phenotype inventory workflow</a>.
+  <a href="https://dockstore.org/workflows/github.com/UW-GAC/primed-inventory-workflows/primed_inventory:main?tab=info">PRIMED phenotype inventory workflow</a>.
   Copy the text in the box below and paste it into the "workspaces" field when running the workflow on AnVIL.
 </p>