Merge pull request #285 from UW-GAC/deploy/stage

Deploy to prod

.github/workflows/ci.yml

@@ -50,7 +50,7 @@ jobs:
         # ahead of planned upgrades we can add versions as
         # needed
         python-version: [3.8]
-        mariadb-version: ["10.3"]
+        mariadb-version: ["10.3", "10.4"]
 
     services:
       mysql:

gregor_django/gregor_anvil/forms.py

@@ -1,10 +1,7 @@
 """Forms classes for the gregor_anvil app."""
 
 from anvil_consortium_manager.forms import Bootstrap5MediaFormMixin
-from dal import autocomplete
 from django import forms
-from django.core.exceptions import ValidationError
-from django.urls import reverse
 
 from . import models
 
@@ -63,139 +60,36 @@ class Meta:
 class CombinedConsortiumDataWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
     """Form for a CombinedConsortiumDataWorkspace object."""
 
-    ERROR_UPLOAD_CYCLE_DOES_NOT_MATCH = (
-        "upload_cycle must match upload_cycle for upload_workspaces."
-    )
-
     class Meta:
         model = models.CombinedConsortiumDataWorkspace
-        fields = ("workspace", "upload_cycle", "upload_workspaces")
-        help_texts = {
-            "upload_workspaces": """Upload workspaces contributing to the combined workspace.
-                                    All upload workspaces must have the same version."""
-        }
-        widgets = {
-            "upload_workspaces": autocomplete.ModelSelect2Multiple(
-                url=reverse(
-                    "anvil_consortium_manager:workspaces:autocomplete_by_type",
-                    args=["upload"],
-                ),
-                attrs={"data-theme": "bootstrap-5"},
-                forward=["upload_cycle"],
-            ),
-        }
-
-    def clean(self):
-        cleaned_data = super().clean()
-        if "upload_cycle" in cleaned_data and "upload_workspaces" in cleaned_data:
-            upload_cycle = cleaned_data["upload_cycle"]
-            upload_workspace_cycles = set(
-                [x.upload_cycle for x in cleaned_data["upload_workspaces"]]
-            )
-            if len(upload_workspace_cycles) > 1:
-                raise ValidationError(self.ERROR_UPLOAD_CYCLE_DOES_NOT_MATCH)
-            x = upload_workspace_cycles.pop()
-            if x != upload_cycle:
-                raise ValidationError(self.ERROR_UPLOAD_CYCLE_DOES_NOT_MATCH)
-
-    # def clean_upload_workspaces(self):
-    #     """Validate that all UploadWorkspaces have the same version."""
-    #     data = self.cleaned_data["upload_workspaces"]
-    #     versions = set([x.version for x in data])
-    #     if len(versions) > 1:
-    #         self.add_error(
-    #             "upload_workspaces",
-    #             ValidationError(self.ERROR_UPLOAD_VERSION_DOES_NOT_MATCH),
-    #         )
-    #     return data
+        fields = (
+            "workspace",
+            "upload_cycle",
+        )
 
 
 class ReleaseWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
     """Form for a ReleaseWorkspace object."""
 
-    ERROR_CONSENT_DOES_NOT_MATCH = (
-        "Consent group must match consent group of upload workspaces."
-    )
-    ERROR_UPLOAD_WORKSPACE_CONSENT = (
-        "Consent group for upload workspaces must be the same."
-    )
-    ERROR_UPLOAD_CYCLE = (
-        "upload_cycle must match upload_cycle of all upload_workspaces."
-    )
-
     class Meta:
         model = models.ReleaseWorkspace
         fields = (
             "upload_cycle",
             "consent_group",
-            "upload_workspaces",
             "full_data_use_limitations",
             "dbgap_version",
             "dbgap_participant_set",
             "date_released",
             "workspace",
         )
         help_texts = {
-            "upload_workspaces": """Upload workspaces contributing to this Release Workspace.
-                                    All upload workspaces must have the same consent group.""",
             "date_released": """Do not select a date for this field unless the workspace has been
                                released to the scientific community.""",
         }
         widgets = {
-            # We considered checkboxes for workspaces with default all checked.
-            # Unfortunately we need to select only those with a given consent, not all workspaces.
-            # So go back to the ModelSelect2Multiple widget.
-            "upload_workspaces": autocomplete.ModelSelect2Multiple(
-                url=reverse(
-                    "anvil_consortium_manager:workspaces:autocomplete_by_type",
-                    args=["upload"],
-                ),
-                attrs={"data-theme": "bootstrap-5"},
-                forward=["consent_group", "upload_cycle"],
-            ),
-            # "date_released": forms.SelectDateInput(),
-            # "date_released": forms.DateInput(),
-            # "date_released": AdminDateWidget(),
             "date_released": CustomDateInput(),
         }
 
-    def clean_upload_workspaces(self):
-        """Validate that all UploadWorkspaces have the same consent group."""
-        data = self.cleaned_data["upload_workspaces"]
-        versions = set([x.consent_group for x in data])
-        upload_cycles = set([x.upload_cycle for x in data])
-        if len(versions) > 1:
-            self.add_error(
-                "upload_workspaces",
-                ValidationError(self.ERROR_UPLOAD_WORKSPACE_CONSENT),
-            )
-        if len(upload_cycles) > 1:
-            self.add_error(
-                "upload_workspaces",
-                ValidationError(self.ERROR_UPLOAD_CYCLE),
-            )
-        return data
-
-    def clean(self):
-        """Validate that consent_group matches the consent group for upload_workspaces."""
-        cleaned_data = super().clean()
-        # Make sure that the consent group specified matches the consent group for the upload_workspaces.
-        consent_group = cleaned_data.get("consent_group")
-        upload_workspaces = cleaned_data.get("upload_workspaces")
-        upload_cycle = cleaned_data.get("upload_cycle")
-        if consent_group and upload_workspaces:
-            # We only need to check the first workspace since the clean_upload_workspaces method checks
-            # that all upload_workspaces have the same consent.
-            if consent_group != upload_workspaces[0].consent_group:
-                raise ValidationError(self.ERROR_CONSENT_DOES_NOT_MATCH)
-        if upload_cycle and upload_workspaces:
-            # We only need to check the first workspace since the clean_upload_workspaces method checks
-            # that all upload_workspaces have the same upload_cycle.
-            if upload_cycle != upload_workspaces[0].upload_cycle:
-                raise ValidationError(self.ERROR_UPLOAD_CYCLE)
-
-        return cleaned_data
-
 
 class DCCProcessingWorkspaceForm(Bootstrap5MediaFormMixin, forms.ModelForm):
     """Form for a DCCProcessingWorkspace object."""

gregor_django/gregor_anvil/migrations/0016_remove_combinedconsortiumdataworkspace_upload_workspaces.py

@@ -0,0 +1,17 @@
+# Generated by Django 3.2.19 on 2023-08-04 22:36
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('gregor_anvil', '0015_dccworkspaces'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='combinedconsortiumdataworkspace',
+            name='upload_workspaces',
+        ),
+    ]

gregor_django/gregor_anvil/migrations/0017_remove_releaseworkspace_upload_workspaces.py

@@ -0,0 +1,17 @@
+# Generated by Django 3.2.19 on 2023-08-07 16:01
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('gregor_anvil', '0016_remove_combinedconsortiumdataworkspace_upload_workspaces'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='releaseworkspace',
+            name='upload_workspaces',
+        ),
+    ]

gregor_django/gregor_anvil/models.py

@@ -151,9 +151,6 @@ class CombinedConsortiumDataWorkspace(TimeStampedModel, BaseWorkspaceData):
     """A model to track a workspace that has data combined from multiple upload workspaces."""
 
     upload_cycle = models.ForeignKey(UploadCycle, on_delete=models.PROTECT)
-    upload_workspaces = models.ManyToManyField(
-        UploadWorkspace, help_text="Upload workspaces"
-    )
 
 
 class ReleaseWorkspace(TimeStampedModel, BaseWorkspaceData):
@@ -168,10 +165,6 @@ class ReleaseWorkspace(TimeStampedModel, BaseWorkspaceData):
         on_delete=models.PROTECT,
     )
     upload_cycle = models.ForeignKey(UploadCycle, on_delete=models.PROTECT)
-    upload_workspaces = models.ManyToManyField(
-        UploadWorkspace,
-        help_text="Upload workspaces contributing data to this workspace.",
-    )
     full_data_use_limitations = models.TextField(
         help_text="The full data use limitations for this workspace."
     )

gregor_django/gregor_anvil/tables.py

@@ -1,6 +1,6 @@
 import django_tables2 as tables
 from anvil_consortium_manager.adapters.workspace import workspace_adapter_registry
-from anvil_consortium_manager.models import Account, Workspace
+from anvil_consortium_manager.models import Account, ManagedGroup, Workspace
 from django.utils.html import format_html
 
 from . import models
@@ -80,20 +80,26 @@ def render_cycle(self, record):
         return str(record)
 
 
-class WorkspaceSharedWithConsortiumTable(tables.Table):
+class WorkspaceConsortiumAccessTable(tables.Table):
     """Table including a column to indicate if a workspace is shared with PRIMED_ALL."""
 
-    is_shared = tables.columns.Column(
+    consortium_access = tables.columns.Column(
         accessor="pk",
-        verbose_name="Shared with GREGoR?",
+        verbose_name="Consortium access?",
         orderable=False,
     )
 
-    def render_is_shared(self, record):
-        is_shared = record.workspacegroupsharing_set.filter(
-            group__name="GREGOR_ALL"
-        ).exists()
-        if is_shared:
+    def render_consortium_access(self, record):
+        try:
+            group = ManagedGroup.objects.get(name="GREGOR_ALL")
+        except ManagedGroup.DoesNotExist:
+            has_consortium_access = False
+        else:
+            has_consortium_access = record.is_in_authorization_domain(
+                group
+            ) and record.is_shared(group)
+
+        if has_consortium_access:
             icon = "check-circle-fill"
             color = "green"
             value = format_html(
@@ -104,7 +110,7 @@ def render_is_shared(self, record):
         return value
 
 
-class DefaultWorkspaceTable(WorkspaceSharedWithConsortiumTable, tables.Table):
+class DefaultWorkspaceTable(WorkspaceConsortiumAccessTable, tables.Table):
     """Class to use for default workspace tables in GREGoR."""
 
     name = tables.Column(linkify=True, verbose_name="Workspace")
@@ -122,12 +128,12 @@ class Meta:
             "name",
             "billing_project",
             "number_groups",
-            "is_shared",
+            "consortium_access",
         )
         order_by = ("name",)
 
 
-class UploadWorkspaceTable(WorkspaceSharedWithConsortiumTable, tables.Table):
+class UploadWorkspaceTable(WorkspaceConsortiumAccessTable, tables.Table):
     """A table for Workspaces that includes fields from UploadWorkspace."""
 
     name = tables.columns.Column(linkify=True)
@@ -140,11 +146,11 @@ class Meta:
             "uploadworkspace__upload_cycle",
             "uploadworkspace__research_center",
             "uploadworkspace__consent_group",
-            "is_shared",
+            "consortium_access",
         )
 
 
-class TemplateWorkspaceTable(WorkspaceSharedWithConsortiumTable, tables.Table):
+class TemplateWorkspaceTable(WorkspaceConsortiumAccessTable, tables.Table):
     """A table for Workspaces that includes fields from TemplateWorkspace."""
 
     name = tables.columns.Column(linkify=True)
@@ -154,7 +160,7 @@ class Meta:
         fields = (
             "name",
             "templateworkspace__intended_use",
-            "is_shared",
+            "consortium_access",
         )
 
 
@@ -177,40 +183,26 @@ def render_workspace_type(self, value):
 
 
 class CombinedConsortiumDataWorkspaceTable(
-    WorkspaceSharedWithConsortiumTable, tables.Table
+    WorkspaceConsortiumAccessTable, tables.Table
 ):
     """A table for Workspaces that includes fields from CombinedConsortiumDataWorkspace."""
 
     name = tables.columns.Column(linkify=True)
     combinedconsortiumdataworkspace__upload_cycle = tables.columns.Column(linkify=True)
-    number_workspaces = tables.columns.Column(
-        accessor="pk",
-        verbose_name="Number of workspaces",
-        orderable=False,
-    )
 
     class Meta:
         model = Workspace
         fields = (
             "name",
             "combinedconsortiumdataworkspace__upload_cycle",
-            "number_workspaces",
         )
 
-    def render_number_workspaces(self, record):
-        return record.combinedconsortiumdataworkspace.upload_workspaces.count()
-
 
 class ReleaseWorkspaceTable(tables.Table):
     """A table for Workspaces that includes fields from ReleaseWorkspace."""
 
     name = tables.columns.Column(linkify=True)
     releaseworkspace__upload_cycle = tables.columns.Column(linkify=True)
-    number_workspaces = tables.columns.Column(
-        accessor="pk",
-        verbose_name="Number of workspaces",
-        orderable=False,
-    )
 
     class Meta:
         model = Workspace
@@ -220,13 +212,9 @@ class Meta:
             "releaseworkspace__consent_group",
             "releaseworkspace__dbgap_version",
             "releaseworkspace__dbgap_participant_set",
-            "number_workspaces",
             "releaseworkspace__date_released",
         )
 
-    def render_number_workspaces(self, record):
-        return record.releaseworkspace.upload_workspaces.count()
-
 
 class DCCProcessingWorkspaceTable(tables.Table):
     """A table for Workspaces that includes fields from DCCProcessingWorkspace."""
@@ -242,7 +230,7 @@ class Meta:
         )
 
 
-class DCCProcessedDataWorkspaceTable(WorkspaceSharedWithConsortiumTable, tables.Table):
+class DCCProcessedDataWorkspaceTable(WorkspaceConsortiumAccessTable, tables.Table):
     """A table for Workspaces that includes fields from DCCProcessedDataWorkspace."""
 
     name = tables.columns.Column(linkify=True)
@@ -254,5 +242,5 @@ class Meta:
             "name",
             "dccprocesseddataworkspace__upload_cycle",
             "dccprocesseddataworkspace__consent_group",
-            "is_shared",
+            "consortium_access",
         )