Introduction of runnable base class to assist with introduction of fitting specs

requirements/dev.txt

@@ -16,8 +16,7 @@ defusedxml==0.5.0         # via python3-openid, social-auth-core
 dj-database-url==0.4.2
 django-braces==1.11.0
 django-guardian==1.4.9
-django==1.11.27
-first==2.0.2              # via pip-tools
+django==1.11.28
 flake8==3.4.1
 gitdb2==2.0.5             # via gitpython
 gitpython==2.1.7

requirements/test.txt

@@ -28,8 +28,8 @@ pycodestyle==2.5.0        # via flake8
 pyflakes==2.1.1           # via flake8
 pyjwt==1.7.1              # via social-auth-core
 pytest-cov==2.5.1
-pytest-django==3.1.2
-pytest==3.2.0
+pytest-django==3.8.0
+pytest==3.6.0
 python3-openid==3.1.0     # via social-auth-core
 pytz==2018.9              # via django
 requests-oauthlib==1.2.0  # via social-auth-core

weblab/conftest.py

@@ -177,7 +177,7 @@ def queued_experiment(model_with_version, protocol_with_version):
         experiment__protocol=protocol_with_version,
         experiment__protocol_version=protocol_with_version.repocache.latest_version,
     )
-    recipes.running_experiment.make(experiment_version=version)
+    recipes.running_experiment.make(runnable=version)
     return version
 
 

weblab/core/recipes.py

@@ -1,19 +1,19 @@
 from model_mommy.recipe import Recipe, foreign_key, seq
 
 
-user = Recipe('accounts.User', institution='UCL')
+user = Recipe('accounts.User', institution='UCL', full_name=seq('test user '))
 
 model = Recipe(
     'ModelEntity',
-    entity_type='model', name=seq('mymodel')
+    entity_type='model', name=seq('my model')
 )
 protocol = Recipe(
     'ProtocolEntity',
-    entity_type='protocol', name=seq('myprotocol')
+    entity_type='protocol', name=seq('my protocol')
 )
 fittingspec = Recipe(
     'FittingSpec',
-    entity_type='fittingspec', name=seq('myspec'),
+    entity_type='fittingspec', name=seq('my spec'),
     protocol=foreign_key(protocol),
 )
 
@@ -38,13 +38,15 @@
     protocol_version=foreign_key(cached_protocol_version),
 )
 
+runnable = Recipe('Runnable')
+
 experiment_version = Recipe('ExperimentVersion', experiment=foreign_key(experiment))
 
-running_experiment = Recipe('RunningExperiment', experiment_version=foreign_key(experiment_version))
+running_experiment = Recipe('RunningExperiment', runnable=foreign_key(runnable))
 
 
 dataset = Recipe('Dataset',
-                 name=seq('mydataset'),
+                 name=seq('my dataset'),
                  protocol=foreign_key(protocol))
 
 dataset_file = Recipe('DatasetFile',

weblab/entities/tests/test_views.py

@@ -431,10 +431,10 @@ def test_complex_visibilities(self, client, logged_in_user, other_user, helpers)
         assert len(interfaces) == 4
 
         expected = {
-            'myprotocol1': {'required': ['p1r2'], 'optional': ['p1o2']},
-            'myprotocol2': {'required': ['p2r2'], 'optional': ['p2o2']},
-            'myprotocol3': {'required': ['p3r1'], 'optional': ['p3o1']},
-            'myprotocol4': {'required': ['p4r3'], 'optional': ['p4o3']},
+            protocol1.name: {'required': ['p1r2'], 'optional': ['p1o2']},
+            protocol2.name: {'required': ['p2r2'], 'optional': ['p2o2']},
+            protocol3.name: {'required': ['p3r1'], 'optional': ['p3o1']},
+            protocol4.name: {'required': ['p4r3'], 'optional': ['p4o3']},
         }
         for iface in interfaces:
             assert iface['name'] in expected
@@ -483,7 +483,7 @@ def test_applies_visibility(self, client, helpers, experiment_version):
         exp.model.set_version_visibility('latest', 'public')
         exp.protocol.set_version_visibility('latest', 'public')
         protocol_version = helpers.add_version(protocol, visibility='private')
-        recipes.experiment_version.make(
+        recipes.runnable.make(
             experiment__protocol=protocol,
             experiment__protocol_version=protocol.repocache.get_version(protocol_version.sha),
             experiment__model=exp.model,
@@ -1666,7 +1666,7 @@ def test_download_archive(self, client, helpers):
         archive = zipfile.ZipFile(BytesIO(response.content))
         assert archive.filelist[0].filename == 'file1.txt'
         assert response['Content-Disposition'] == (
-            'attachment; filename=%s_%s.zip' % (model.name, commit.sha)
+            'attachment; filename=%s_%s.zip' % (model.name.replace(' ', '_'), commit.sha)
         )
 
     def test_returns_404_if_no_commits_yet(self, logged_in_user, client):
@@ -2115,7 +2115,7 @@ def test_view_run_experiment_model(self, client, helpers, logged_in_user):
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': protocol.pk,
                                                     'entity': protocol,
-                                                    'name': 'myprotocol1',
+                                                    'name': protocol.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
@@ -2147,14 +2147,14 @@ def test_view_run_experiment_model_multiple_users(self, client, helpers, logged_
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': protocol.pk,
                                                     'entity': protocol,
-                                                    'name': 'myprotocol1',
+                                                    'name': protocol.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
         assert response.context['other_object_list'] == [
             {'id': other_protocol.pk,
              'entity': other_protocol,
-             'name': 'myprotocol2',
+             'name': other_protocol.name,
              'versions': [{'commit': other_version2, 'tags': ['v1'], 'latest': True},
                           {'commit': other_version1, 'tags': [], 'latest': False}]},
         ]
@@ -2179,7 +2179,7 @@ def test_view_run_experiment_model_post(self, client, helpers, logged_in_user):
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': protocol.pk,
                                                     'entity': protocol,
-                                                    'name': 'myprotocol1',
+                                                    'name': protocol.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
@@ -2229,7 +2229,7 @@ def test_view_run_experiment_model_post_exclude_existing(self, client, helpers,
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': protocol.pk,
                                                     'entity': protocol,
-                                                    'name': 'myprotocol1',
+                                                    'name': protocol.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
@@ -2281,14 +2281,14 @@ def test_view_run_experiment_post_model_multiple_users(self, client, helpers, lo
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': protocol.pk,
                                                     'entity': protocol,
-                                                    'name': 'myprotocol1',
+                                                    'name': protocol.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
         assert response.context['other_object_list'] == [
             {'id': other_protocol.pk,
              'entity': other_protocol,
-             'name': 'myprotocol2',
+             'name': other_protocol.name,
              'versions': [{'commit': other_version2, 'tags': ['v1'], 'latest': True},
                           {'commit': other_version1, 'tags': [], 'latest': False}]},
         ]
@@ -2338,7 +2338,7 @@ def test_view_run_experiment_model_not_latest(self, client, helpers, logged_in_u
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': protocol.pk,
                                                     'entity': protocol,
-                                                    'name': 'myprotocol1',
+                                                    'name': protocol.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
@@ -2384,7 +2384,7 @@ def test_view_run_experiment_protocol(self, client, helpers, logged_in_user):
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': model.pk,
                                                     'entity': model,
-                                                    'name': 'mymodel1',
+                                                    'name': model.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
@@ -2416,14 +2416,14 @@ def test_view_run_experiment_protocol_multiple_users(self, client, helpers, logg
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': model.pk,
                                                     'entity': model,
-                                                    'name': 'mymodel1',
+                                                    'name': model.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
         assert response.context['other_object_list'] == [
             {'id': other_model.pk,
              'entity': other_model,
-             'name': 'mymodel2',
+             'name': other_model.name,
              'versions': [{'commit': other_version2, 'tags': ['v1'], 'latest': True},
                           {'commit': other_version1, 'tags': [], 'latest': False}]},
         ]
@@ -2446,7 +2446,7 @@ def test_view_run_experiment_protocol_post(self, client, helpers, logged_in_user
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': model.pk,
                                                     'entity': model,
-                                                    'name': 'mymodel1',
+                                                    'name': model.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
@@ -2502,7 +2502,7 @@ def test_view_run_experiment_protocol_post_exclude_existing(self, client, helper
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': model.pk,
                                                     'entity': model,
-                                                    'name': 'mymodel1',
+                                                    'name': model.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
@@ -2551,14 +2551,14 @@ def test_view_run_experiment_post_protocol_multiple_users(self, client, helpers,
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': model.pk,
                                                     'entity': model,
-                                                    'name': 'mymodel1',
+                                                    'name': model.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
         assert response.context['other_object_list'] == [
             {'id': other_model.pk,
              'entity': other_model,
-             'name': 'mymodel2',
+             'name': other_model.name,
              'versions': [{'commit': other_version2, 'tags': ['v1'], 'latest': True},
                           {'commit': other_version1, 'tags': [], 'latest': False}]},
         ]
@@ -2605,7 +2605,7 @@ def test_view_run_experiment_none_checked(self, client, helpers, logged_in_user)
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': protocol.pk,
                                                     'entity': protocol,
-                                                    'name': 'myprotocol1',
+                                                    'name': protocol.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]
@@ -2653,7 +2653,7 @@ def test_view_run_experiment_protocol_not_latest(self, client, helpers, logged_i
         assert response.status_code == 200
         assert response.context['object_list'] == [{'id': model.pk,
                                                     'entity': model,
-                                                    'name': 'mymodel1',
+                                                    'name': model.name,
                                                     'versions': [{'commit': version2, 'tags': ['v1'], 'latest': True},
                                                                  {'commit': version1, 'tags': [], 'latest': False}]},
                                                    ]

weblab/entities/views.py

@@ -663,7 +663,7 @@ def check_access_token(self, token):
         """
         from entities.models import AnalysisTask
         from experiments.models import RunningExperiment
-        entity_field = 'experiment_version__experiment__%s' % self.kwargs['entity_type']
+        entity_field = 'runnable__experimentversion__experiment__%s' % self.kwargs['entity_type']
         self_id = self._get_object().id
         return (RunningExperiment.objects.filter(
             id=token,

weblab/experiments/apps.py

@@ -1,14 +1,14 @@
 from django.apps import AppConfig
 from django.db.models.signals import pre_delete
 
-from .signals import experiment_version_deleted, running_experiment_deleted
+from .signals import runnable_deleted, running_experiment_deleted
 
 
 class ExperimentsConfig(AppConfig):
     name = 'experiments'
 
     def ready(self):
-        from .models import ExperimentVersion, RunningExperiment
+        from .models import Runnable, RunningExperiment
 
-        pre_delete.connect(experiment_version_deleted, ExperimentVersion)
+        pre_delete.connect(runnable_deleted, Runnable)
         pre_delete.connect(running_experiment_deleted, RunningExperiment)

weblab/experiments/emails.py

@@ -3,15 +3,15 @@
 from django.template.loader import render_to_string
 
 
-def send_experiment_finished_email(experiment_version):
-    author = experiment_version.author
+def send_experiment_finished_email(runnable):
+    author = runnable.author
 
     if author.receive_emails:
         body = render_to_string(
             'emails/experiment_finished.txt',
             {
                 'user': author,
-                'experiment_version': experiment_version,
+                'runnable': runnable,
                 'base_url': settings.BASE_URL,
             }
         )

weblab/experiments/migrations/0025_auto_20200316_1652.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.20 on 2020-03-16 16:52
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0024_merge_20200211_0929'),
+    ]
+
+    operations = [
+        migrations.RenameModel(
+            old_name='ExperimentVersion',
+            new_name='Runnable',
+        ),
+        migrations.RemoveIndex(
+            model_name='runnable',
+            name='experiments_created_00e2f1_idx',
+        ),
+        migrations.AddIndex(
+            model_name='runnable',
+            index=models.Index(fields=['created_at'], name='experiments_created_a4e4b7_idx'),
+        ),
+    ]

weblab/experiments/migrations/0026_experimentversion.py

@@ -0,0 +1,27 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.20 on 2020-03-16 17:00
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0025_auto_20200316_1652'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='ExperimentVersion',
+            fields=[
+                ('runnable_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='experiments.Runnable')),
+                ('experiment_key', models.ForeignKey(default=None, null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='versions_copy', to='experiments.Experiment')),
+            ],
+            options={
+                'abstract': False,
+            },
+            bases=('experiments.runnable',),
+        ),
+    ]

weblab/experiments/migrations/0027_move_runnable.py

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.20 on 2020-03-16 17:02
+from __future__ import unicode_literals
+
+from django.db import migrations
+
+
+
+def runnable_to_exp_version(apps, schema_editor):
+    ExperimentVersion = apps.get_model('experiments', 'ExperimentVersion')
+    Runnable = apps.get_model('experiments', 'Runnable')
+    for runnable in Runnable.objects.all():
+        experiment_version = ExperimentVersion(runnable_ptr=runnable,
+                                               experiment_key_id=runnable.experiment_id)
+        experiment_version.save_base(raw=True)
+
+
+def exp_version_to_runnable(apps, schema_editor):
+    ExperimentVersion = apps.get_model('experiments', 'ExperimentVersion')
+    Runnable = apps.get_model('experiments', 'Runnable')
+    for experiment_version in ExperimentVersion.objects.all():
+        runnable = experiment_version.runnable_ptr
+        runnable.experiment_id = experiment_version.experiment_key_id
+        runnable.save()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('experiments', '0026_experimentversion'),
+    ]
+
+    operations = [
+        migrations.RunPython(runnable_to_exp_version, exp_version_to_runnable),
+    ]