Merge branch 'dabih-release' into devfix-simple-postgresql

chemreg/common/models.py

@@ -1,17 +1,38 @@
+from django.conf import settings
 from django.db import models
 
+from chemreg.common.utils import get_current_user_pk
+
 
 class CommonInfo(models.Model):
     """Common information to be applied to all models.
 
     Attributes:
         created_at (datetime.datetime): When the model was created.
+        created_by (chemreg.user.models.User): Who created this model.
         updated_at (datetime.datetime): When the model was updated.
+        updated_by (chemreg.user.models.User): Who updated this model.
 
     """
 
-    created_at = models.DateTimeField(auto_now_add=True)
-    updated_at = models.DateTimeField(auto_now=True)
+    created_at = models.DateTimeField(auto_now_add=True, editable=False)
+    created_by = models.ForeignKey(
+        settings.AUTH_USER_MODEL,
+        default=get_current_user_pk,
+        editable=False,
+        related_name="%(class)s_created_by_set",
+        null=True,
+        on_delete=models.PROTECT,
+    )
+    updated_at = models.DateTimeField(auto_now=True, editable=False)
+    updated_by = models.ForeignKey(
+        settings.AUTH_USER_MODEL,
+        editable=False,
+        related_name="%(class)s_updated_by_set",
+        null=True,
+        on_delete=models.PROTECT,
+    )
 
     class Meta:
         abstract = True
+        ordering = ["pk"]

chemreg/common/signals.py

@@ -0,0 +1,17 @@
+from django.db.models.signals import pre_save
+from django.dispatch import receiver
+
+from chemreg.common.models import CommonInfo
+from chemreg.common.utils import get_current_user_pk
+
+
+@receiver(pre_save)
+def set_updated_by(sender, instance, **kwargs):
+    """Signal to set the `CommonInfo.updated_by`.
+
+    Arguments:
+        sender: the model class.
+        instance: the model instance.
+    """
+    if isinstance(instance, CommonInfo):
+        instance.updated_by_id = get_current_user_pk()

chemreg/common/tests.py

@@ -1,5 +1,8 @@
 from django.db import models
 
+import pytest
+from crum import impersonate
+
 from chemreg.common.models import CommonInfo
 
 
@@ -21,3 +24,19 @@ def test_commoninfo_attr():
 def test_inherits_commoninfo(chemreg_model):
     """Test that all ChemReg models inherit CommonInfo."""
     assert issubclass(chemreg_model, CommonInfo)
+
+
+@pytest.mark.django_db
+def test_user_link(user_factory):
+    """Test that created_by/updated_by are saved."""
+    user_1 = user_factory()
+    assert user_1.created_by_id is None
+    assert user_1.updated_by_id is None
+    with impersonate(user_1):
+        user_2 = user_factory()
+        assert user_2.created_by_id == user_1.pk
+        assert user_2.updated_by_id == user_1.pk
+    with impersonate(user_2):
+        user_2.save()
+        assert user_2.created_by_id == user_1.pk
+        assert user_2.updated_by_id == user_2.pk

chemreg/common/utils.py

@@ -0,0 +1,13 @@
+from crum import get_current_user
+
+
+def get_current_user_pk():
+    """Retrieve the current user's primary key.
+
+    Returns:
+        The primary key of the current request's user.
+    """
+    current_user = get_current_user()
+    if not current_user:
+        return None
+    return current_user.pk

chemreg/compound/migrations/0001_initial.py

@@ -0,0 +1,228 @@
+# Generated by Django 3.0.3 on 2020-03-25 17:38
+
+import django.db.models.deletion
+from django.conf import settings
+from django.db import migrations, models
+
+import computed_property.fields
+
+import chemreg.common.utils
+import chemreg.compound.models
+import chemreg.compound.utils
+import chemreg.compound.validators
+
+
+def fwd_create_illdefined_querystructuretype(apps, schema_editor):
+    QueryStructureType = apps.get_model("compound", "QueryStructureType")
+    db_alias = schema_editor.connection.alias
+    QueryStructureType.objects.using(db_alias).create(
+        name="ill-defined",
+        label="Ill defined",
+        short_description="Ill defined",
+        long_description="Ill defined",
+    )
+
+
+def rev_create_illdefined_querystructuretype(apps, schema_editor):
+    QueryStructureType = apps.get_model("compound", "QueryStructureType")
+    db_alias = schema_editor.connection.alias
+    QueryStructureType.objects.using(db_alias).filter(name="ill-defined").delete()
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        ("contenttypes", "0002_remove_content_type_name"),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="BaseCompound",
+            fields=[
+                (
+                    "id",
+                    models.AutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("created_at", models.DateTimeField(auto_now_add=True)),
+                ("updated_at", models.DateTimeField(auto_now=True)),
+                (
+                    "cid",
+                    models.CharField(
+                        default=chemreg.compound.utils.build_cid,
+                        max_length=50,
+                        unique=True,
+                        validators=[
+                            chemreg.compound.validators.validate_cid_regex,
+                            chemreg.compound.validators.validate_cid_checksum,
+                        ],
+                    ),
+                ),
+                ("structure", models.TextField()),
+                (
+                    "created_by",
+                    models.ForeignKey(
+                        default=chemreg.common.utils.get_current_user_pk,
+                        editable=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.PROTECT,
+                        related_name="basecompound_created_by_set",
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+                (
+                    "polymorphic_ctype",
+                    models.ForeignKey(
+                        editable=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="polymorphic_compound.basecompound_set+",
+                        to="contenttypes.ContentType",
+                    ),
+                ),
+                (
+                    "updated_by",
+                    models.ForeignKey(
+                        editable=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.PROTECT,
+                        related_name="basecompound_updated_by_set",
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+            ],
+            options={"ordering": ["pk"], "abstract": False,},
+        ),
+        migrations.CreateModel(
+            name="DefinedCompound",
+            fields=[
+                (
+                    "basecompound_ptr",
+                    models.OneToOneField(
+                        auto_created=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        parent_link=True,
+                        primary_key=True,
+                        serialize=False,
+                        to="compound.BaseCompound",
+                    ),
+                ),
+                (
+                    "inchikey",
+                    computed_property.fields.ComputedCharField(
+                        compute_from="_inchikey", editable=False, max_length=29
+                    ),
+                ),
+            ],
+            options={"ordering": ["pk"], "abstract": False,},
+            bases=("compound.basecompound",),
+        ),
+        migrations.CreateModel(
+            name="QueryStructureType",
+            fields=[
+                (
+                    "id",
+                    models.AutoField(
+                        auto_created=True,
+                        primary_key=True,
+                        serialize=False,
+                        verbose_name="ID",
+                    ),
+                ),
+                ("created_at", models.DateTimeField(auto_now_add=True)),
+                ("updated_at", models.DateTimeField(auto_now=True)),
+                (
+                    "name",
+                    models.SlugField(
+                        help_text="Query structure type name",
+                        max_length=49,
+                        unique=True,
+                        verbose_name="name",
+                    ),
+                ),
+                (
+                    "label",
+                    models.CharField(
+                        help_text="Query structure type label",
+                        max_length=99,
+                        unique=True,
+                        verbose_name="label",
+                    ),
+                ),
+                (
+                    "short_description",
+                    models.CharField(
+                        help_text="Query structure type short description",
+                        max_length=499,
+                        verbose_name="short description",
+                    ),
+                ),
+                (
+                    "long_description",
+                    models.TextField(
+                        help_text="Query structure type long description",
+                        verbose_name="long description",
+                    ),
+                ),
+                (
+                    "created_by",
+                    models.ForeignKey(
+                        default=chemreg.common.utils.get_current_user_pk,
+                        editable=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.PROTECT,
+                        related_name="querystructuretype_created_by_set",
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+                (
+                    "updated_by",
+                    models.ForeignKey(
+                        editable=False,
+                        null=True,
+                        on_delete=django.db.models.deletion.PROTECT,
+                        related_name="querystructuretype_updated_by_set",
+                        to=settings.AUTH_USER_MODEL,
+                    ),
+                ),
+            ],
+            options={"ordering": ["pk"], "abstract": False,},
+        ),
+        migrations.RunPython(
+            fwd_create_illdefined_querystructuretype,
+            rev_create_illdefined_querystructuretype,
+        ),
+        migrations.CreateModel(
+            name="IllDefinedCompound",
+            fields=[
+                (
+                    "basecompound_ptr",
+                    models.OneToOneField(
+                        auto_created=True,
+                        on_delete=django.db.models.deletion.CASCADE,
+                        parent_link=True,
+                        primary_key=True,
+                        serialize=False,
+                        to="compound.BaseCompound",
+                    ),
+                ),
+                (
+                    "query_structure_type",
+                    models.ForeignKey(
+                        default=chemreg.compound.models.get_illdefined_qst,
+                        on_delete=django.db.models.deletion.PROTECT,
+                        to="compound.QueryStructureType",
+                    ),
+                ),
+            ],
+            options={"verbose_name": "ill-defined compound",},
+            bases=("compound.basecompound",),
+        ),
+    ]