Volumes: add volume ontology class

Add an ontology class for volumes, create class instances for all
existing volumes, and relate volume class instances to volume rows via a
`volume_class_instance` table. Also move the `model_of` relation from
the needed classes for the tracing tool to the default project needed
classes.

Written with @tomka, @clbarnes, and @Willp24.

See #1765.

django/applications/catmaid/control/project.py

@@ -23,7 +23,8 @@
     'annotation': "An arbitrary annotation",
     'stack_property': 'A property which a stack has',
     'landmark': "A particular type of location",
-    "landmarkgroup": "A type of collection that groups landmarks"
+    "landmarkgroup": "A type of collection that groups landmarks",
+    'volume': 'A region of space'
 }
 
 # All relations needed by the tracing system alongside their
@@ -34,6 +35,7 @@
     'annotated_with': "Something is annotated by something else.",
     'has_property': 'A thing which has an arbitrary property',
     'close_to': 'Something is spatially in the neighborhood of something else',
+    'model_of': "Marks something as a model of something else."
 }
 
 # All client datastores needed by the tracing system along their descriptions.

django/applications/catmaid/control/tracing.py

@@ -28,7 +28,6 @@
 needed_relations = {
     'labeled_as': "Something is labeled by sth. else.",
     'element_of': "A generic element-of relationship",
-    'model_of': "Marks something as a model of something else.",
     'presynaptic_to': "Something is presynaptic to something else.",
     'postsynaptic_to': "Something is postsynaptic to something else.",
     'abutting': "Two things abut against each other",

django/applications/catmaid/migrations/0051_create_volume_class_and_instances.py

@@ -0,0 +1,133 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.14 on 2018-07-20 14:27
+from __future__ import unicode_literals
+
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+import django.utils.timezone
+
+from catmaid.apps import get_system_user
+
+
+def forwards(apps, schema_editor):
+    """Make sure all required class and relations are existing for all
+    projects.  We can't use the regular model classes, but have to get
+    them through the migration system.
+    """
+    from catmaid.control.project import validate_project_setup
+
+    Class = apps.get_model('catmaid', 'Class')
+    Project = apps.get_model('catmaid', 'Project')
+    Relation = apps.get_model('catmaid', 'Relation')
+    User = apps.get_model('auth', 'User')
+    ClientDatastore = apps.get_model('catmaid', 'ClientDatastore')
+
+    projects = Project.objects.all()
+    # If there are no projects, don't continue, because there is nothing to
+    # migrate.
+    if 0 == len(projects) or 0 == User.objects.count():
+        return
+
+    system_user = get_system_user(User)
+    for p in projects:
+        validate_project_setup(p.id, system_user.id, True, Class, Relation, ClientDatastore)
+
+forward_create_relations = """
+    CREATE TABLE volume_class_instance (
+        volume_id bigint NOT NULL,
+        class_instance_id integer NOT NULL
+    )
+    INHERITS (relation_instance);
+
+    -- Volume Class Instance constraints
+    ALTER TABLE ONLY volume_class_instance
+    ADD CONSTRAINT volume_class_instance_pkey PRIMARY KEY (id);
+
+    ALTER TABLE ONLY volume_class_instance
+    ADD CONSTRAINT volume_class_instance_sa_id
+    FOREIGN KEY (volume_id)
+    REFERENCES catmaid_volume(id) DEFERRABLE INITIALLY DEFERRED;
+
+    ALTER TABLE ONLY volume_class_instance
+    ADD CONSTRAINT volume_class_instance_id_fkey
+    FOREIGN KEY (class_instance_id)
+    REFERENCES class_instance(id) DEFERRABLE INITIALLY DEFERRED;
+
+    WITH new_cis AS (
+        INSERT INTO class_instance (user_id, project_id, name, class_id)
+        SELECT
+            v.user_id,
+            v.project_id,
+            v.name,
+            c.id
+        FROM catmaid_volume v
+        JOIN class c ON (c.project_id = v.project_id AND c.class_name = 'volume')
+        RETURNING id, user_id, project_id, name
+    )
+    INSERT INTO volume_class_instance (user_id, project_id, relation_id, volume_id, class_instance_id)
+    SELECT
+        v.user_id,
+        v.project_id,
+        r.id,
+        v.id,
+        ci.id
+    FROM catmaid_volume v
+    JOIN relation r ON (r.project_id = v.project_id AND r.relation_name = 'model_of')
+    JOIN new_cis ci ON (
+        ci.user_id = v.user_id AND
+        ci.project_id = v.project_id AND
+        ci.name = v.name
+    );
+
+    -- Create history tables
+    SELECT create_history_table('volume_class_instance'::regclass, 'edition_time', 'txid');
+"""
+
+backward_create_relations = """
+    SELECT disable_history_tracking_for_table('volume_class_instance'::regclass,
+        get_history_table_name('volume_class_instance'::regclass));
+    SELECT drop_history_table('volume_class_instance'::regclass);
+
+    DROP TABLE volume_class_instance;
+
+    DELETE FROM class_instance
+    USING class c
+    WHERE class_instance.class_id = c.id
+        AND c.class_name = 'volume';
+
+"""
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('catmaid', '0050_ensure_system_user'),
+    ]
+
+    operations = [
+        migrations.RunPython(forwards, migrations.RunPython.noop),
+        migrations.RunSQL(
+            forward_create_relations,
+            backward_create_relations,
+            [
+                migrations.CreateModel(
+                    name='VolumeClassInstance',
+                    fields=[
+                        ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                        ('creation_time', models.DateTimeField(default=django.utils.timezone.now)),
+                        ('edition_time', models.DateTimeField(default=django.utils.timezone.now)),
+                        ('class_instance', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='catmaid.ClassInstance')),
+                        ('project', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='catmaid.Project')),
+                        ('relation', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='catmaid.Relation')),
+                        ('user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)),
+                        ('volume', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='catmaid.Volume')),
+                    ],
+                    options={
+                        'db_table': 'volume_class_instance',
+                    },
+                ),
+            ]
+        ),
+    ]

django/applications/catmaid/models.py

@@ -719,6 +719,17 @@ class Volume(UserFocusedModel):
     geometry = spatial_models.GeometryField(dim=3, srid=0)
 
 
+class VolumeClassInstance(UserFocusedModel):
+    # Repeat the columns inherited from 'relation_instance'
+    relation = models.ForeignKey(Relation, on_delete=models.CASCADE)
+    # Now new columns:
+    volume = models.ForeignKey(Volume, on_delete=models.CASCADE)
+    class_instance = models.ForeignKey(ClassInstance, on_delete=models.CASCADE)
+
+    class Meta:
+        db_table = "volume_class_instance"
+
+
 class RegionOfInterest(UserFocusedModel):
     # Repeat the columns inherited from 'location'
     editor = models.ForeignKey(User, on_delete=models.CASCADE,