Deploy to staging

config/settings/base.py

@@ -308,6 +308,8 @@
     "cdsa:records:studies",
     "cdsa:records:workspaces",
     "cdsa:records:user_access",
+    "dbgap:records:index",
+    "dbgap:records:applications",
 ]
 
 # django-dbbackup
@@ -372,6 +374,7 @@
     "primed.dbgap.adapters.dbGaPWorkspaceAdapter",
     "primed.cdsa.adapters.CDSAWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.ConsortiumDevelWorkspaceAdapter",
+    "primed.miscellaneous_workspaces.adapters.DataPrepWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.ExampleWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.SimulatedDataWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.OpenAccessWorkspaceAdapter",

primed/cdsa/views.py

@@ -2,8 +2,8 @@
 
 from anvil_consortium_manager.anvil_api import AnVILAPIError
 from anvil_consortium_manager.auth import (
-    AnVILConsortiumManagerEditRequired,
-    AnVILConsortiumManagerViewRequired,
+    AnVILConsortiumManagerStaffEditRequired,
+    AnVILConsortiumManagerStaffViewRequired,
     AnVILProjectManagerAccess,
 )
 from anvil_consortium_manager.models import GroupAccountMembership, ManagedGroup
@@ -26,7 +26,7 @@
 
 
 class AgreementMajorVersionDetail(
-    AnVILConsortiumManagerViewRequired, MultiTableMixin, DetailView
+    AnVILConsortiumManagerStaffViewRequired, MultiTableMixin, DetailView
 ):
     """Display a "detail" page for an agreement major version (e.g., 1.x)."""
 
@@ -59,7 +59,7 @@ def get_context_data(self, **kwargs):
         context = super().get_context_data(**kwargs)
         context["show_deprecation_message"] = not self.object.is_valid
         edit_permission_codename = "anvil_consortium_manager." + (
-            AnVILProjectManagerAccess.EDIT_PERMISSION_CODENAME
+            AnVILProjectManagerAccess.STAFF_EDIT_PERMISSION_CODENAME
         )
         context[
             "show_invalidate_button"
@@ -70,7 +70,7 @@ def get_context_data(self, **kwargs):
 
 
 class AgreementMajorVersionInvalidate(
-    AnVILConsortiumManagerEditRequired, SuccessMessageMixin, UpdateView
+    AnVILConsortiumManagerStaffEditRequired, SuccessMessageMixin, UpdateView
 ):
     """A view to invalidate an AgreementMajorVersion instance.
 
@@ -132,7 +132,7 @@ def get_success_url(self):
 
 
 class AgreementVersionDetail(
-    AnVILConsortiumManagerViewRequired, SingleTableMixin, DetailView
+    AnVILConsortiumManagerStaffViewRequired, SingleTableMixin, DetailView
 ):
     """Display a "detail" page for an agreement major/minor version (e.g., 1.3)."""
 
@@ -167,14 +167,14 @@ def get_context_data(self, **kwargs):
         return context
 
 
-class AgreementVersionList(AnVILConsortiumManagerViewRequired, SingleTableView):
+class AgreementVersionList(AnVILConsortiumManagerStaffViewRequired, SingleTableView):
     """Display a list of AgreementVersions."""
 
     model = models.AgreementVersion
     table_class = tables.AgreementVersionTable
 
 
-class SignedAgreementList(AnVILConsortiumManagerViewRequired, SingleTableView):
+class SignedAgreementList(AnVILConsortiumManagerStaffViewRequired, SingleTableView):
     """Display a list of SignedAgreement objects."""
 
     model = models.SignedAgreement
@@ -294,7 +294,7 @@ def get_success_url(self):
 
 
 class MemberAgreementCreate(
-    AnVILConsortiumManagerEditRequired,
+    AnVILConsortiumManagerStaffEditRequired,
     AgreementTypeCreateMixin,
     SuccessMessageMixin,
     FormView,
@@ -311,7 +311,7 @@ class MemberAgreementCreate(
 
 
 class DataAffiliateAgreementCreate(
-    AnVILConsortiumManagerEditRequired,
+    AnVILConsortiumManagerStaffEditRequired,
     AgreementTypeCreateMixin,
     SuccessMessageMixin,
     FormView,
@@ -348,7 +348,7 @@ def get_agreement_type(self, form, formset):
         return agreement_type
 
 
-class MemberAgreementDetail(AnVILConsortiumManagerViewRequired, DetailView):
+class MemberAgreementDetail(AnVILConsortiumManagerStaffViewRequired, DetailView):
     """View to show details about a `MemberAgreement`."""
 
     model = models.MemberAgreement
@@ -371,23 +371,23 @@ def get_context_data(self, **kwargs):
             "show_deprecation_message"
         ] = not self.object.signed_agreement.version.major_version.is_valid
         edit_permission_codename = "anvil_consortium_manager." + (
-            AnVILProjectManagerAccess.EDIT_PERMISSION_CODENAME
+            AnVILProjectManagerAccess.STAFF_EDIT_PERMISSION_CODENAME
         )
         context["show_update_button"] = self.request.user.has_perm(
             edit_permission_codename
         )
         return context
 
 
-class MemberAgreementList(AnVILConsortiumManagerViewRequired, SingleTableView):
+class MemberAgreementList(AnVILConsortiumManagerStaffViewRequired, SingleTableView):
     """Display a list of MemberAgreement objects."""
 
     model = models.MemberAgreement
     table_class = tables.MemberAgreementTable
 
 
 class SignedAgreementStatusUpdate(
-    AnVILConsortiumManagerEditRequired, SuccessMessageMixin, UpdateView
+    AnVILConsortiumManagerStaffEditRequired, SuccessMessageMixin, UpdateView
 ):
 
     model = models.SignedAgreement
@@ -411,7 +411,7 @@ def get_object(self, queryset=None):
         return obj
 
 
-class DataAffiliateAgreementDetail(AnVILConsortiumManagerViewRequired, DetailView):
+class DataAffiliateAgreementDetail(AnVILConsortiumManagerStaffViewRequired, DetailView):
     """View to show details about a `DataAffiliateAgreement`."""
 
     model = models.DataAffiliateAgreement
@@ -434,23 +434,25 @@ def get_context_data(self, **kwargs):
             "show_deprecation_message"
         ] = not self.object.signed_agreement.version.major_version.is_valid
         edit_permission_codename = "anvil_consortium_manager." + (
-            AnVILProjectManagerAccess.EDIT_PERMISSION_CODENAME
+            AnVILProjectManagerAccess.STAFF_EDIT_PERMISSION_CODENAME
         )
         context["show_update_button"] = self.request.user.has_perm(
             edit_permission_codename
         )
         return context
 
 
-class DataAffiliateAgreementList(AnVILConsortiumManagerViewRequired, SingleTableView):
+class DataAffiliateAgreementList(
+    AnVILConsortiumManagerStaffViewRequired, SingleTableView
+):
     """Display a list of DataAffiliateAgreement objects."""
 
     model = models.DataAffiliateAgreement
     table_class = tables.DataAffiliateAgreementTable
 
 
 class NonDataAffiliateAgreementCreate(
-    AnVILConsortiumManagerEditRequired,
+    AnVILConsortiumManagerStaffEditRequired,
     AgreementTypeCreateMixin,
     SuccessMessageMixin,
     FormView,
@@ -466,7 +468,9 @@ class NonDataAffiliateAgreementCreate(
     ERROR_CREATING_GROUP = "Error creating access group on AnVIL."
 
 
-class NonDataAffiliateAgreementDetail(AnVILConsortiumManagerViewRequired, DetailView):
+class NonDataAffiliateAgreementDetail(
+    AnVILConsortiumManagerStaffViewRequired, DetailView
+):
     """View to show details about a `NonDataAffiliateAgreement`."""
 
     model = models.NonDataAffiliateAgreement
@@ -489,7 +493,7 @@ def get_context_data(self, **kwargs):
             "show_deprecation_message"
         ] = not self.object.signed_agreement.version.major_version.is_valid
         edit_permission_codename = "anvil_consortium_manager." + (
-            AnVILProjectManagerAccess.EDIT_PERMISSION_CODENAME
+            AnVILProjectManagerAccess.STAFF_EDIT_PERMISSION_CODENAME
         )
         context["show_update_button"] = self.request.user.has_perm(
             edit_permission_codename
@@ -498,15 +502,15 @@ def get_context_data(self, **kwargs):
 
 
 class NonDataAffiliateAgreementList(
-    AnVILConsortiumManagerViewRequired, SingleTableView
+    AnVILConsortiumManagerStaffViewRequired, SingleTableView
 ):
     """Display a list of NonDataAffiliateAgreement objects."""
 
     model = models.NonDataAffiliateAgreement
     table_class = tables.NonDataAffiliateAgreementTable
 
 
-class SignedAgreementAudit(AnVILConsortiumManagerViewRequired, TemplateView):
+class SignedAgreementAudit(AnVILConsortiumManagerStaffViewRequired, TemplateView):
     """View to show audit results for `SignedAgreements`."""
 
     template_name = "cdsa/signedagreement_audit.html"
@@ -538,7 +542,7 @@ def get_context_data(self, **kwargs):
         return context
 
 
-class CDSAWorkspaceAudit(AnVILConsortiumManagerViewRequired, TemplateView):
+class CDSAWorkspaceAudit(AnVILConsortiumManagerStaffViewRequired, TemplateView):
     """View to show audit results for `CDSAWorkspaces`."""
 
     template_name = "cdsa/cdsaworkspace_audit.html"

primed/dbgap/tables.py

@@ -330,3 +330,40 @@ class Meta:
         model = models.dbGaPDataAccessRequest
         fields = ("dbgap_dac", "dbgap_current_status", "total")
         attrs = {"class": "table table-sm"}
+
+
+class dbGaPApplicationRecordsTable(tables.Table):
+    """Class to render a publicly-viewable table of dbGaPApplication objects."""
+
+    dbgap_project_id = tables.columns.Column()
+    principal_investigator = tables.columns.Column(
+        verbose_name="Application PI",
+        accessor="principal_investigator__name",
+    )
+    principal_investigator__study_sites = tables.columns.ManyToManyColumn(
+        verbose_name="Study site(s)",
+    )
+    number_approved_dars = tables.columns.ManyToManyColumn(
+        accessor="dbgapdataaccesssnapshot_set",
+        filter=lambda qs: qs.filter(is_most_recent=True),
+        verbose_name="Number of approved DARs",
+        transform=lambda obj: obj.dbgapdataaccessrequest_set.approved().count(),
+    )
+    number_requested_dars = tables.columns.ManyToManyColumn(
+        accessor="dbgapdataaccesssnapshot_set",
+        filter=lambda qs: qs.filter(is_most_recent=True),
+        verbose_name="Number of requested DARs",
+        transform=lambda obj: obj.dbgapdataaccessrequest_set.count(),
+    )
+    last_update = ManyToManyDateTimeColumn(
+        accessor="dbgapdataaccesssnapshot_set",
+        filter=lambda qs: qs.filter(is_most_recent=True),
+    )
+
+    class Meta:
+        model = models.dbGaPApplication
+        fields = (
+            "dbgap_project_id",
+            "principal_investigator",
+        )
+        order_by = ("dbgap_project_id",)