Merged fixes for issues 1262, 1432, 1514, 1524 and 1552

docker-compose.yml

@@ -106,7 +106,7 @@ services:
       OIDC_RENEW_ID_TOKEN_EXPIRY_MINUTES: '210'
       # Public target access strings?
       # A comma-separated list of Project titles.
-      PUBLIC_TAS: lb18145-1
+      PUBLIC_TAS: ${PUBLIC_TAS:-lb18145-1}
       # Squonk configuration
       SQUONK2_VERIFY_CERTIFICATES: 'No'
       SQUONK2_UNIT_BILLING_DAY: 3

viewer/cset_upload.py

@@ -293,7 +293,7 @@ def create_mol(self, inchi, target, name=None) -> Compound:
                 smiles=Chem.MolToSmiles(sanitized_mol),
                 inchi=inchi,
                 inchi_key=inchi_key,
-                current_identifier=name,
+                description=name,
             )
             # This is a new compound.
             cpd.save()
@@ -317,27 +317,23 @@ def create_mol(self, inchi, target, name=None) -> Compound:
 
         return cpd
 
-    def set_props(self, cpd, props, compound_set) -> List[ScoreDescription]:
+    def set_props(self, cpd, props, score_descriptions) -> List[ScoreDescription]:
         if 'ref_mols' and 'ref_pdb' not in list(props.keys()):
             raise Exception('ref_mols and ref_pdb not set!')
-        set_obj = ScoreDescription.objects.filter(computed_set=compound_set)
-        assert set_obj
-
-        set_props_list = [s.name for s in set_obj]
-        for key in list(props.keys()):
-            if key in set_props_list not in ['ref_mols', 'ref_pdb', 'original SMILES']:
-                if dataType(str(props[key])) == 'TEXT':
-                    score_value = TextScoreValues()
-                else:
-                    score_value = NumericalScoreValues()
-                score_value.score = ScoreDescription.objects.get(
-                    computed_set=compound_set, name=key
-                )
-                score_value.value = props[key]
-                score_value.compound = cpd
-                score_value.save()
 
-        return set_obj
+        for sd in score_descriptions:
+            logger.debug('sd: %s', sd)
+            if dataType(str(props[sd.name])) == 'TEXT':
+                score_value = TextScoreValues()
+            else:
+                score_value = NumericalScoreValues()
+
+            score_value.value = props[sd.name]
+            score_value.compound = cpd
+            score_value.score = sd
+            score_value.save()
+
+        return score_descriptions
 
     def set_mol(
         self, mol, target, compound_set, filename, zfile=None, zfile_hashvals=None
@@ -550,15 +546,22 @@ def get_submission_info(self, description_mol) -> ComputedSetSubmitter:
         )[0]
 
     def process_mol(
-        self, mol, target, compound_set, filename, zfile=None, zfile_hashvals=None
+        self,
+        mol,
+        target,
+        compound_set,
+        filename,
+        score_descriptions,
+        zfile=None,
+        zfile_hashvals=None,
     ) -> List[ScoreDescription]:
         cpd = self.set_mol(mol, target, compound_set, filename, zfile, zfile_hashvals)
         other_props = mol.GetPropsAsDict()
-        return self.set_props(cpd, other_props, compound_set)
+        return self.set_props(cpd, other_props, score_descriptions)
 
     def set_descriptions(
         self, filename, computed_set: ComputedSet
-    ) -> List[Chem.rdchem.Mol]:
+    ) -> tuple[List[Chem.rdchem.Mol], List[ScoreDescription]]:
         suppl = Chem.SDMolSupplier(str(filename))
         description_mol = suppl[0]
 
@@ -577,6 +580,9 @@ def set_descriptions(
         computed_set.save()
 
         description_dict = description_mol.GetPropsAsDict()
+        # score descriptions for this upload, doesn't matter if
+        # created or existing
+        score_descriptions = []
         for key in description_dict.keys():
             if key in descriptions_needed and key not in [
                 'ref_mols',
@@ -585,13 +591,14 @@ def set_descriptions(
                 'Name',
                 'original SMILES',
             ]:
-                _ = ScoreDescription.objects.get_or_create(
+                description, _ = ScoreDescription.objects.get_or_create(
                     computed_set=computed_set,
                     name=key,
                     description=description_dict[key],
                 )
+                score_descriptions.append(description)
 
-        return mols
+        return mols, score_descriptions
 
     def task(self) -> ComputedSet:
         # Truncate submitted method (lower-case)?
@@ -673,7 +680,7 @@ def task(self) -> ComputedSet:
         # This also sets the submitter and method URL properties of the computed set
         # while also saving it.
         sdf_filename = str(self.sdf_filename)
-        mols_to_process = self.set_descriptions(
+        mols_to_process, score_descriptions = self.set_descriptions(
             filename=sdf_filename, computed_set=computed_set
         )
 
@@ -688,14 +695,21 @@ def task(self) -> ComputedSet:
                 self.target_id,
                 computed_set,
                 sdf_filename,
+                score_descriptions,
                 self.zfile,
                 self.zfile_hashvals,
             )
 
         # move and save the compound set
-        new_filename = f'{settings.MEDIA_ROOT}{settings.COMPUTED_SET_MEDIA_DIRECTORY}/{computed_set.name}.sdf'
+        new_filename = (
+            Path(settings.MEDIA_ROOT)
+            .joinpath(settings.COMPUTED_SET_MEDIA_DIRECTORY)
+            .joinpath(
+                f'{computed_set.name}_upload_{computed_set.md_ordinal}_{Path(sdf_filename).name}'
+            )
+        )
         os.rename(sdf_filename, new_filename)
-        computed_set.submitted_sdf = sdf_filename
+        computed_set.submitted_sdf = Path(sdf_filename).name
         computed_set.written_sdf_filename = new_filename
         computed_set.save()
 

viewer/migrations/0065_compound_ligand_name.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.25 on 2024-10-18 09:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0064_auto_20240918_1256'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='compound',
+            name='ligand_name',
+            field=models.TextField(blank=True, default='LIG'),
+        ),
+    ]

viewer/migrations/0073_historicalcomputedset.py

@@ -0,0 +1,49 @@
+# Generated by Django 3.2.25 on 2024-11-04 10:27
+
+from django.conf import settings
+from django.db import migrations, models
+import django.db.models.deletion
+import simple_history.models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('viewer', '0072_auto_20241010_1437'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='HistoricalComputedSet',
+            fields=[
+                ('name', models.CharField(db_index=True, max_length=50)),
+                ('submitted_sdf', models.TextField(help_text='The original SDF containing the ComputedSet', max_length=255)),
+                ('written_sdf_filename', models.TextField(help_text='The written ComputedSet filename', max_length=1000, null=True)),
+                ('spec_version', models.FloatField(help_text='The version of the SDF file format specification')),
+                ('method_url', models.TextField(help_text='A url linking to a write-up of the methodology used to create the computed set', max_length=1000, null=True)),
+                ('method', models.CharField(blank=True, help_text='The name of the algorithmic method used to generate the compounds (e.g. Fragmenstein)', max_length=50, null=True)),
+                ('upload_date', models.DateField(blank=True, help_text='The date the set was uploaded', null=True)),
+                ('md_ordinal', models.SmallIntegerField(blank=True, help_text='The ordinal distinguishing between uploads using the same method and date', null=True)),
+                ('upload_task_id', models.CharField(help_text='The task ID of the upload Celery task', max_length=50, null=True)),
+                ('upload_status', models.CharField(choices=[('PENDING', 'PENDING'), ('STARTED', 'STARTED'), ('SUCCESS', 'SUCCESS'), ('FAILURE', 'FAILURE'), ('RETRY', 'RETRY'), ('REVOKED', 'REVOKED')], help_text='Status of the upload. Only be updated at the end of the process', max_length=7, null=True)),
+                ('upload_progress', models.DecimalField(decimal_places=2, help_text='Intended to be used as an indication of progress (0 to 100%)', max_digits=5, null=True)),
+                ('upload_datetime', models.DateTimeField(help_text='The datetime the upload was completed', null=True)),
+                ('history_id', models.AutoField(primary_key=True, serialize=False)),
+                ('history_date', models.DateTimeField(db_index=True)),
+                ('history_change_reason', models.CharField(max_length=100, null=True)),
+                ('history_type', models.CharField(choices=[('+', 'Created'), ('~', 'Changed'), ('-', 'Deleted')], max_length=1)),
+                ('history_user', models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='+', to=settings.AUTH_USER_MODEL)),
+                ('owner_user', models.ForeignKey(blank=True, db_constraint=False, default=1, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to=settings.AUTH_USER_MODEL)),
+                ('submitter', models.ForeignKey(blank=True, db_constraint=False, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='viewer.computedsetsubmitter')),
+                ('target', models.ForeignKey(blank=True, db_constraint=False, null=True, on_delete=django.db.models.deletion.DO_NOTHING, related_name='+', to='viewer.target')),
+            ],
+            options={
+                'verbose_name': 'historical computed set',
+                'verbose_name_plural': 'historical computed sets',
+                'ordering': ('-history_date', '-history_id'),
+                'get_latest_by': ('history_date', 'history_id'),
+            },
+            bases=(simple_history.models.HistoricalChanges, models.Model),
+        ),
+    ]

viewer/migrations/0073_merge_20241018_0956.py

@@ -0,0 +1,14 @@
+# Generated by Django 3.2.25 on 2024-10-18 09:56
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0065_compound_ligand_name'),
+        ('viewer', '0072_auto_20241010_1437'),
+    ]
+
+    operations = [
+    ]

viewer/migrations/0073_merge_20241028_1554.py

@@ -0,0 +1,14 @@
+# Generated by Django 3.2.25 on 2024-10-28 15:54
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0065_compound_ligand_name'),
+        ('viewer', '0072_auto_20241010_1437'),
+    ]
+
+    operations = [
+    ]

viewer/migrations/0074_auto_20241018_1028.py

@@ -0,0 +1,46 @@
+# Generated by Django 3.2.25 on 2024-10-18 10:28
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0073_merge_20241018_0956'),
+    ]
+
+    def temporary_name(apps, schema_editor):
+        CompoundIdentifier = apps.get_model('viewer', 'CompoundIdentifier')
+
+        for idf in CompoundIdentifier.objects.all():
+            idf.name_type = idf.type.name
+            idf.save()
+
+    def reverse_temporary_name(apps, schema_editor):
+        pass
+
+
+    # this contains some edits, the automatically constructed
+    # migration was not in the correct order, so I had to move things
+    # around to preserve data
+    operations = [
+        migrations.AddField(
+            model_name='compoundidentifier',
+            name='name_type',
+            field=models.TextField(null=True),
+        ),
+        migrations.RunPython(temporary_name, reverse_temporary_name),
+        migrations.RemoveField(
+            model_name='compoundidentifier',
+            name='type',
+        ),
+        migrations.RemoveField(
+            model_name='compoundidentifiertype',
+            name='id',
+        ),
+        migrations.AlterField(
+            model_name='compoundidentifiertype',
+            name='name',
+            field=models.TextField(primary_key=True, serialize=False),
+        ),
+    ]

viewer/migrations/0074_auto_20241028_1617.py

@@ -0,0 +1,33 @@
+# Generated by Django 3.2.25 on 2024-10-28 16:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0073_merge_20241028_1554'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='compound',
+            name='modeled_smiles_canon',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='modeled_smiles_soakdb',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='soaked_smiles_canon',
+            field=models.TextField(blank=True, null=True),
+        ),
+        migrations.AddField(
+            model_name='compound',
+            name='soaked_smiles_soakdb',
+            field=models.TextField(blank=True, null=True),
+        ),
+    ]

viewer/migrations/0075_remove_compoundidentifier_type.py

@@ -0,0 +1,31 @@
+# Generated by Django 3.2.25 on 2024-10-18 10:38
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0074_auto_20241018_1028'),
+    ]
+
+    def relink_type(apps, schema_editor):
+        CompoundIdentifier = apps.get_model('viewer', 'CompoundIdentifier')
+        CompoundIdentifierType = apps.get_model('viewer', 'CompoundIdentifierType')
+
+        for idf in CompoundIdentifier.objects.all():
+            idf.type = CompoundIdentifierType.objects.get(name=idf.name_type)
+            idf.save()
+
+    def reverse_relink_type(apps, schema_editor):
+        pass
+
+    operations = [
+        migrations.AddField(
+            model_name='compoundidentifier',
+            name='type',
+            field=models.ForeignKey(null=True, to_field='name', on_delete=django.db.models.deletion.CASCADE, to='viewer.compoundidentifiertype'),
+        ),
+        migrations.RunPython(relink_type, reverse_relink_type),
+    ]

viewer/migrations/0076_compoundidentifier_type.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.25 on 2024-10-18 10:39
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0075_remove_compoundidentifier_type'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='compoundidentifier',
+            name='name_type',
+        ),
+    ]

viewer/migrations/0077_alter_compoundidentifier_type.py

@@ -0,0 +1,19 @@
+# Generated by Django 3.2.25 on 2024-10-18 10:40
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0076_compoundidentifier_type'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='compoundidentifier',
+            name='type',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='viewer.compoundidentifiertype'),
+        ),
+    ]