Merge pull request #675 from UW-GAC/bugfix/inventory-inputs-for-multi…

…ple-studies

Fix bug where only a single study is shown for a workspace linked to multiple studies

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:
     {
@@ -212,7 +212,8 @@ def get_workspaces_for_phenotype_inventory():
 
     # Combine all querysets and process into the expected output for the AnVIL workflow.
     workspaces = dbgap_workspaces.union(cdsa_workspaces).union(open_access_workspaces)
-
+    # Sort by workspace_name so that itertools.groupby works as expected.
+    workspaces = sorted(workspaces, key=lambda x: x["workspace_name"])
     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]

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>