Merge pull request #400 from UW-GAC/feature/collab-analysis-workspaces

Collaborative analysis workspaces

add_collaborative_analysis_example_data.py

@@ -0,0 +1,117 @@
+"""Temporary script to create some example data for the collaborative_analysis app.
+
+Run with: python manage.py shell < add_collaborative_analysis_example_data.py
+"""
+
+from anvil_consortium_manager.tests.factories import (
+    AccountFactory,
+    BillingProjectFactory,
+    GroupAccountMembershipFactory,
+    GroupGroupMembershipFactory,
+    ManagedGroupFactory,
+)
+
+from primed.cdsa.tests.factories import CDSAWorkspaceFactory
+from primed.collaborative_analysis.tests.factories import (
+    CollaborativeAnalysisWorkspaceFactory,
+)
+from primed.dbgap.tests.factories import dbGaPWorkspaceFactory
+from primed.miscellaneous_workspaces.tests.factories import OpenAccessWorkspaceFactory
+
+billing_project = BillingProjectFactory.create(name="test_collab")
+
+# Create some collaborative analysis workspace.
+# Workspace 1
+collaborative_analysis_workspace_1 = CollaborativeAnalysisWorkspaceFactory.create(
+    workspace__name="collab_1_open_access", workspace__billing_project=billing_project
+)
+source_workspace_1_1 = OpenAccessWorkspaceFactory.create(
+    workspace__name="source_1_open_access", workspace__billing_project=billing_project
+)
+collaborative_analysis_workspace_1.source_workspaces.add(source_workspace_1_1.workspace)
+
+# Workspace 2
+collaborative_analysis_workspace_2 = CollaborativeAnalysisWorkspaceFactory.create(
+    workspace__name="collab_2_dbgap_and_cdsa",
+    workspace__billing_project=billing_project,
+)
+source_workspace_2_1 = dbGaPWorkspaceFactory.create(
+    workspace__name="source_2_dbgap", workspace__billing_project=billing_project
+)
+collaborative_analysis_workspace_2.source_workspaces.add(source_workspace_2_1.workspace)
+source_workspace_2_2 = CDSAWorkspaceFactory.create(
+    workspace__name="source_2_cdsa", workspace__billing_project=billing_project
+)
+collaborative_analysis_workspace_2.source_workspaces.add(source_workspace_2_2.workspace)
+
+# Workspace 3 - with an error
+collaborative_analysis_workspace_3 = CollaborativeAnalysisWorkspaceFactory.create(
+    workspace__name="collab_3_with_error", workspace__billing_project=billing_project
+)
+source_workspace_3_1 = OpenAccessWorkspaceFactory.create(
+    workspace__name="source_3_open_access", workspace__billing_project=billing_project
+)
+collaborative_analysis_workspace_3.source_workspaces.add(source_workspace_3_1.workspace)
+
+
+# Add accounts to the auth domains.
+account_1 = AccountFactory.create(
+    user__name="Adrienne", verified=True, email="[email protected]"
+)
+account_2 = AccountFactory.create(
+    user__name="Ben", verified=True, email="[email protected]"
+)
+account_3 = AccountFactory.create(
+    user__name="Matt", verified=True, email="[email protected]"
+)
+account_4 = AccountFactory.create(
+    user__name="Stephanie", verified=True, email="[email protected]"
+)
+
+# Set up collab analysis workspace one
+# analyst group
+GroupAccountMembershipFactory.create(
+    account=account_1, group=collaborative_analysis_workspace_1.analyst_group
+)
+GroupAccountMembershipFactory.create(
+    account=account_2, group=collaborative_analysis_workspace_1.analyst_group
+)
+# auth domains
+GroupAccountMembershipFactory.create(
+    account=account_1,
+    group=collaborative_analysis_workspace_1.workspace.authorization_domains.first(),
+)
+
+# Set up collab analysis workspace two
+# analyst group
+GroupAccountMembershipFactory.create(
+    account=account_3, group=collaborative_analysis_workspace_2.analyst_group
+)
+GroupAccountMembershipFactory.create(
+    account=account_4, group=collaborative_analysis_workspace_2.analyst_group
+)
+# auth domains
+GroupAccountMembershipFactory.create(
+    account=account_3,
+    group=collaborative_analysis_workspace_2.workspace.authorization_domains.first(),
+)
+GroupAccountMembershipFactory.create(
+    account=account_3,
+    group=source_workspace_2_1.workspace.authorization_domains.first(),
+)
+GroupAccountMembershipFactory.create(
+    account=account_3,
+    group=source_workspace_2_2.workspace.authorization_domains.first(),
+)
+GroupAccountMembershipFactory.create(
+    account=account_4,
+    group=source_workspace_2_1.workspace.authorization_domains.first(),
+)
+
+# Set up collab analysis workspace three
+# Managed group to show an error
+managed_group = ManagedGroupFactory.create(name="test-error")
+GroupGroupMembershipFactory.create(
+    parent_group=collaborative_analysis_workspace_3.workspace.authorization_domains.first(),
+    child_group=managed_group,
+)

config/settings/base.py

@@ -96,6 +96,7 @@
     "primed.miscellaneous_workspaces",
     "primed.duo",
     "primed.cdsa",
+    "primed.collaborative_analysis",
 ]
 
 # https://docs.djangoproject.com/en/dev/ref/settings/#installed-apps
@@ -376,6 +377,7 @@
     "primed.miscellaneous_workspaces.adapters.SimulatedDataWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.ResourceWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.ConsortiumDevelWorkspaceAdapter",
+    "primed.collaborative_analysis.adapters.CollaborativeAnalysisWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.TemplateWorkspaceAdapter",
     "primed.miscellaneous_workspaces.adapters.DataPrepWorkspaceAdapter",
 ]

config/urls.py

@@ -26,6 +26,12 @@
     path("dbgap/", include("primed.dbgap.urls", namespace="dbgap")),
     path("duo/", include("primed.duo.urls", namespace="duo")),
     path("cdsa/", include("primed.cdsa.urls", namespace="cdsa")),
+    path(
+        "collaborative_analysis/",
+        include(
+            "primed.collaborative_analysis.urls", namespace="collaborative_analysis"
+        ),
+    ),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
 
 

primed/cdsa/tests/factories.py

@@ -122,7 +122,9 @@ def authorization_domains(self, create, extracted, **kwargs):
             return
 
         # Create an authorization domain.
-        auth_domain = ManagedGroupFactory.create()
+        auth_domain = ManagedGroupFactory.create(
+            name="auth_{}".format(self.workspace.name)
+        )
         self.workspace.authorization_domains.add(auth_domain)
 
     class Meta:

primed/collaborative_analysis/adapters.py

@@ -0,0 +1,20 @@
+from anvil_consortium_manager.adapters.workspace import BaseWorkspaceAdapter
+from anvil_consortium_manager.forms import WorkspaceForm
+
+from . import forms, models, tables
+
+
+class CollaborativeAnalysisWorkspaceAdapter(BaseWorkspaceAdapter):
+    """Adapter for CollaborativeAnalysisWorkspace."""
+
+    type = "collab_analysis"
+    name = "Collaborative Analysis workspace"
+    description = "Workspaces used for collaborative analyses"
+    list_table_class_staff_view = tables.CollaborativeAnalysisWorkspaceStaffTable
+    list_table_class_view = tables.CollaborativeAnalysisWorkspaceUserTable
+    workspace_form_class = WorkspaceForm
+    workspace_data_model = models.CollaborativeAnalysisWorkspace
+    workspace_data_form_class = forms.CollaborativeAnalysisWorkspaceForm
+    workspace_detail_template_name = (
+        "collaborative_analysis/collaborativeanalysisworkspace_detail.html"
+    )

primed/collaborative_analysis/admin.py

@@ -0,0 +1,21 @@
+from django.contrib import admin
+from simple_history.admin import SimpleHistoryAdmin
+
+from . import models
+
+
+@admin.register(models.CollaborativeAnalysisWorkspace)
+class CollaborativeAnalysisWorkspaceAdmin(SimpleHistoryAdmin):
+    """Admin class for the `CollaborativeAnalysisWorkspace` model."""
+
+    list_display = (
+        "id",
+        "workspace",
+        "custodian",
+    )
+    list_filter = ("proposal_id",)
+    sortable_by = (
+        "id",
+        "workspace",
+        "custodian",
+    )

primed/collaborative_analysis/apps.py

@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class CollabAnalysisConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "primed.collaborative_analysis"