Merge pull request #169 from UW-GAC/deploy/stage

Deploy/stage
UW-GAC · Mar 24, 2023 · 4fe583e · 4fe583e
2 parents adf205f + c0e6522
commit 4fe583e
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Showing 10 changed files with 46 additions and 2 deletions.
diff --git a/config/settings/base.py b/config/settings/base.py
@@ -203,7 +203,6 @@
                 "django.template.context_processors.tz",
                 "django.contrib.messages.context_processors.messages",
                 "primed.utils.context_processors.settings_context",
-                "anvil_consortium_manager.context_processors.workspace_adapter",
             ],
         },
     }

diff --git a/primed-apps-activate.sh b/primed-apps-activate.sh
@@ -0,0 +1,7 @@
+export DJANGO_SITE_DIR=/var/www/django/primed_apps/
+export DJANGO_SITE_USER=primedweb
+export DJANGO_SETTINGS_MODULE=config.settings.apps
+export DJANGO_WSGI_FILE=config/primed_apps_wsgi.py
+export GAC_ENV=primed_apps
+cd $DJANGO_SITE_DIR
+. venv/bin/activate
diff --git a/primed-apps-dev-activate.sh b/primed-apps-dev-activate.sh
@@ -0,0 +1,11 @@
+# Sets environment variables, changes directory and activates venv
+# for gregor apps dev env
+# Used by crontab, validate any changes
+
+export DJANGO_SITE_DIR=/var/www/django/primed_apps_dev/
+export DJANGO_SITE_USER=primedweb
+export DJANGO_SETTINGS_MODULE=config.settings.apps_dev
+export DJANGO_WSGI_FILE=config/primed_apps_dev_wsgi.py
+export GAC_ENV=primed_apps_dev
+cd $DJANGO_SITE_DIR
+. venv/bin/activate
diff --git a/primed/dbgap/adapters.py b/primed/dbgap/adapters.py
@@ -8,6 +8,7 @@ class dbGaPWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "dbgap"
     name = "dbGaP workspace"
+    description = "Workspaces containing data from released dbGaP accessions"
     list_table_class = tables.dbGaPWorkspaceTable
     workspace_data_model = models.dbGaPWorkspace
     workspace_data_form_class = forms.dbGaPWorkspaceForm

diff --git a/primed/dbgap/tests/test_views.py b/primed/dbgap/tests/test_views.py
@@ -1029,6 +1029,7 @@ def get_api_json_response(
                 ],
                 "name": workspace,
                 "namespace": billing_project,
+                "isLocked": False,
             },
         }
         return json_data

diff --git a/primed/miscellaneous_workspaces/adapters.py b/primed/miscellaneous_workspaces/adapters.py
@@ -11,6 +11,7 @@ class SimulatedDataWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "simulated_data"
     name = "Simulated Data workspace"
+    description = "Workspaces containing simulated data"
     list_table_class = WorkspaceTable
     workspace_data_model = models.SimulatedDataWorkspace
     workspace_data_form_class = forms.SimulatedDataWorkspaceForm
@@ -24,6 +25,7 @@ class ConsortiumDevelWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "devel"
     name = "Consortium development workspace"
+    description = "Workspaces intended for consortium development of methods"
     list_table_class = WorkspaceTable
     workspace_data_model = models.ConsortiumDevelWorkspace
     workspace_data_form_class = forms.ConsortiumDevelWorkspaceForm
@@ -35,6 +37,9 @@ class ExampleWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "example"
     name = "Example workspace"
+    description = (
+        "Workspaces containing examples of using AnVIL, working with data, etc."
+    )
     list_table_class = WorkspaceTable
     workspace_data_model = models.ExampleWorkspace
     workspace_data_form_class = forms.ExampleWorkspaceForm
@@ -46,6 +51,7 @@ class TemplateWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "template"
     name = "Template workspace"
+    description = "Template workspaces that can be cloned to create other workspaces"
     list_table_class = WorkspaceTable
     workspace_data_model = models.TemplateWorkspace
     workspace_data_form_class = forms.TemplateWorkspaceForm
@@ -57,6 +63,7 @@ class OpenAccessWorkspaceAdapter(BaseWorkspaceAdapter):
 
     type = "open_access"
     name = "Open access workspace"
+    description = "Workspaces containing open access data"
     list_table_class = tables.OpenAccessWorkspaceTable
     workspace_data_model = models.OpenAccessWorkspace
     workspace_data_form_class = forms.OpenAccessWorkspaceForm

diff --git a/primed/miscellaneous_workspaces/tests/test_views.py b/primed/miscellaneous_workspaces/tests/test_views.py
@@ -166,6 +166,7 @@ def get_api_json_response(
                 ],
                 "name": workspace,
                 "namespace": billing_project,
+                "isLocked": False,
             },
         }
         return json_data
@@ -388,6 +389,7 @@ def get_api_json_response(
                 ],
                 "name": workspace,
                 "namespace": billing_project,
+                "isLocked": False,
             },
         }
         return json_data
@@ -610,6 +612,7 @@ def get_api_json_response(
                 ],
                 "name": workspace,
                 "namespace": billing_project,
+                "isLocked": False,
             },
         }
         return json_data
@@ -831,6 +834,7 @@ def get_api_json_response(
                 ],
                 "name": workspace,
                 "namespace": billing_project,
+                "isLocked": False,
             },
         }
         return json_data
@@ -1066,6 +1070,7 @@ def get_api_json_response(
                 ],
                 "name": workspace,
                 "namespace": billing_project,
+                "isLocked": False,
             },
         }
         return json_data

diff --git a/primed_apps.cron b/primed_apps.cron
@@ -0,0 +1,6 @@
+# PRIMED_APPS crontab
+# nightly except sunday at 01:00
+0 1 * * MON-SAT . /var/www/django/primed_apps/primed-apps-activate.sh; python manage.py run_anvil_audit --email [email protected] --errors-only >> cron.log 2>&1
+
+# sunday night at 01:00
+0 1 * * SUN . /var/www/django/primed_apps/primed-apps-activate.sh; python manage.py run_anvil_audit --email [email protected] >> cron.log 2>&1
diff --git a/primed_apps_dev.cron b/primed_apps_dev.cron
@@ -0,0 +1,7 @@
+# PRIMED_APPS_DEV crontab - disabled by default
+# can be enabled for testing.
+# nightly except sunday at 01:00
+# 0 1 * * MON-SAT . /var/www/django/primed_apps_dev/primed-apps-dev-activate.sh; python manage.py run_anvil_audit --email [email protected] --errors-only >> cron.log 2>&1
+
+# sunday night at 01:00
+# 0 1 * * SUN . /var/www/django/primed_apps_dev/primed-apps-dev-activate.sh; python manage.py run_anvil_audit --email [email protected] >> cron.log 2>&1
diff --git a/requirements/base.txt b/requirements/base.txt
@@ -22,7 +22,7 @@ django-dbbackup==4.0.1 # https://github.com/jazzband/django-dbbackup
 django-extensions==3.2.1  # https://github.com/django-extensions/django-extensions
 
 # anvil_consortium_manager
-git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.12.1
+git+https://github.com/UW-GAC/django-anvil-consortium-manager.git@v0.14
 
 # Simple history - model history tracking
 django-simple-history==3.1.1