Merge pull request #400 from xchem/staging

Fixes for 944, 1065 and 1066
xchem · Jun 20, 2023 · 6807884 · 6807884
2 parents ad808ce + d1ca76b
commit 6807884
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Showing 7 changed files with 319 additions and 19 deletions.
diff --git a/api/urls.py b/api/urls.py
@@ -87,6 +87,7 @@
 router.register(r"job_file_transfer", viewer_views.JobFileTransferView, basename='job_file_transfer')
 router.register(r"job_callback", viewer_views.JobCallBackView, basename='job_callback')
 router.register(r"job_config", viewer_views.JobConfigView, basename='job_config')
+router.register(r"job_override", viewer_views.JobOverrideView, basename='job_override')
 
 from rest_framework_swagger.renderers import OpenAPIRenderer, SwaggerUIRenderer
 from rest_framework.decorators import api_view, renderer_classes

diff --git a/viewer/download_structures.py b/viewer/download_structures.py
@@ -463,11 +463,12 @@ def _create_structures_zip(target,
             errors += _molecule_files_zip(zip_contents, ziparchive,
                                           combined_sdf_file, error_file)
 
-        # Add combined_sdf_file to the archive.
-        combined_sdf_file_exists = os.path.isfile(combined_sdf_file)
-
-        if zip_contents['molecules']['single_sdf_file'] is True \
-                and combined_sdf_file_exists:
+        # Add combined_sdf_file to the archive?
+        if (
+            zip_contents['molecules']['single_sdf_file'] is True
+            and combined_sdf_file
+            and os.path.isfile(combined_sdf_file)
+        ):
             ziparchive.write(
                 combined_sdf_file,
                 os.path.join(_ZIP_FILEPATHS['single_sdf_file'],

diff --git a/viewer/migrations/0032_add_job_override_table.py b/viewer/migrations/0032_add_job_override_table.py
@@ -0,0 +1,28 @@
+# Generated by Django 3.1.14 on 2023-05-31 13:44
+
+from django.conf import settings
+import django.core.serializers.json
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('viewer', '0031_fix_JobFileTransfer_sub_path'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='JobOverride',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('override', models.JSONField(encoder=django.core.serializers.json.DjangoJSONEncoder)),
+                ('author', models.ForeignKey(help_text='The user that uploaded the override', null=True, on_delete=django.db.models.deletion.SET_NULL, to=settings.AUTH_USER_MODEL)),
+            ],
+            options={
+                'db_table': 'viewer_joboverride',
+            },
+        ),
+    ]
diff --git a/viewer/models.py b/viewer/models.py
@@ -1223,6 +1223,16 @@ def job_has_finished(self):
         """
         return self.job_status in [JobRequest.SUCCESS, JobRequest.FAILURE, 'LOST']
 
+
+class JobOverride(models.Model):
+    override = models.JSONField(encoder=DjangoJSONEncoder)
+    author = models.ForeignKey(User, null=True, on_delete=models.SET_NULL,
+                               help_text="The user that uploaded the override")
+
+    class Meta:
+        db_table = 'viewer_joboverride'
+
+
 class Squonk2Org(models.Model):
     """Django model to store Squonk2 Organisations (UUIDs) and the Account Servers
     they belong to. Managed by the Squonk2Agent class.

diff --git a/viewer/serializers.py b/viewer/serializers.py
@@ -28,7 +28,8 @@
     MoleculeTag,
     SessionProjectTag,
     JobFileTransfer,
-    JobRequest
+    JobRequest,
+    JobOverride
 )
 from viewer.utils import get_https_host
 
@@ -789,3 +790,14 @@ class Meta:
         fields = ("job_status", "state_transition_time")
 
 # End of Serializers for Squonk Jobs
+
+class JobOverrideReadSerializer(serializers.ModelSerializer):
+    class Meta:
+        model = JobOverride
+        fields = '__all__'
+
+
+class JobOverrideWriteSerializer(serializers.ModelSerializer):
+    class Meta:
+        model = JobOverride
+        fields = ('override',)
diff --git a/viewer/squonk/day-1-job-override.json b/viewer/squonk/day-1-job-override.json
@@ -0,0 +1,191 @@
+{
+    "global": {
+      "job_dir": "fragalysis-jobs/{username}/{job_name}-{timestamp}",
+      "protein_id": "{selected_protein}"
+    },
+    "precompilation_ignore": ["job_dir", "protein_id"],
+    "fragalysis-jobs": [
+      {
+        "job_collection": "fragmenstein",
+        "job_name": "fragmenstein-combine",
+        "job_version": "1.0.0",
+        "inputs": {
+          "fragments": {
+            "type": "array",
+            "uniqueItems": true,
+            "format": "chemical/x-mdl-molfile",
+            "items": {
+              "from": "lhs",
+              "enum": "{inputs_dir}/{target}-{item}.mol",
+              "enumNames": "{item}"
+            }
+          },
+          "protein": {
+            "type": "string",
+            "format": "chemical/x-pdb",
+            "from": "lhs",
+            "enum": "{inputs_dir}/{target}-{item}_apo-desolv.pdb",
+            "enumNames": "{item}"
+          }
+        },
+        "options": {
+          "outfile": {
+            "default": "{job_dir}/merged.sdf",
+            "ui:widget": "hidden"
+          },
+          "count": {
+            "type": "integer",
+            "default": 5
+          },
+          "smilesFieldName": {
+            "type": "string",
+            "default": "original SMILES",
+            "ui:widget": "hidden"
+          },
+          "fragIdField": {
+            "type": "string",
+            "default": "_Name",
+            "ui:widget": "hidden"
+          },
+          "proteinFieldName": {
+            "type": "string",
+            "default": "ref_pdb",
+            "ui:widget": "hidden"
+          },
+          "proteinFieldValue": {
+            "type": "string",
+            "default": "{protein_id}",
+            "ui:widget": "hidden"
+          }
+        },
+        "outputs": {
+          "outputs": { "type": "string" }
+        },
+        "results": ["Merged molecules"]
+      },
+
+      {
+        "job_collection": "fragmenstein",
+        "job_name": "fragmenstein-combine-multi-scoring",
+        "job_version": "1.0.0",
+        "inputs": {
+          "fragments": {
+            "type": "array",
+            "uniqueItems": true,
+            "format": "chemical/x-mdl-molfile",
+            "items": {
+              "from": "lhs",
+              "enum": "{inputs_dir}/{target}-{item}.mol",
+              "enumNames": "{item}"
+            }
+          },
+          "protein": {
+            "type": "string",
+            "format": "chemical/x-pdb",
+            "from": "lhs",
+            "enum": "{inputs_dir}/{target}-{item}_apo-desolv.pdb",
+            "enumNames": "{item}"
+          }
+        },
+        "options": {
+          "outfile": {
+            "default": "{job_dir}/merged.sdf",
+            "ui:widget": "hidden"
+          },
+          "count": {
+            "type": "integer",
+            "default": 5
+          },
+          "smilesFieldName": {
+            "type": "string",
+            "default": "original SMILES",
+            "ui:widget": "hidden"
+          },
+          "fragIdField": {
+            "type": "string",
+            "default": "_Name",
+            "ui:widget": "hidden"
+          },
+          "proteinFieldName": {
+            "type": "string",
+            "default": "ref_pdb",
+            "ui:widget": "hidden"
+          },
+          "proteinFieldValue": {
+            "type": "string",
+            "value": "{protein_id}",
+            "ui:widget": "hidden"
+          }
+        },
+        "outputs": {
+          "outputs": { "type": "string" }
+        },
+        "results": ["Merged molecules"]
+      },
+
+      {
+        "job_collection": "fragmenstein",
+        "job_name": "fragmenstein-place-string",
+        "job_version": "1.0.0",
+        "inputs": {
+          "fragments": {
+            "type": "array",
+            "uniqueItems": true,
+            "format": "chemical/x-mdl-molfile",
+            "items": {
+              "from": "lhs",
+              "enum": "{inputs_dir}/{target}-{item}.mol",
+              "enumNames": "{item}"
+            }
+          },
+          "protein": {
+            "type": "string",
+            "format": "chemical/x-pdb",
+            "from": "lhs",
+            "enum": "{inputs_dir}/{target}-{item}_apo-desolv.pdb",
+            "enumNames": "{item}"
+          }
+        },
+        "options": {
+          "outfile": {
+            "default": "{job_dir}/merged.sdf",
+            "ui:widget": "hidden"
+          },
+          "count": {
+            "type": "integer",
+            "default": 5
+          },
+          "smilesFieldName": {
+            "type": "string",
+            "default": "original SMILES",
+            "ui:widget": "hidden"
+          },
+          "smiles": {
+            "items": {
+              "ui:widget": "textarea"
+            }
+          },
+          "fragIdField": {
+            "type": "string",
+            "default": "_Name",
+            "ui:widget": "hidden"
+          },
+          "proteinFieldName": {
+            "type": "string",
+            "default": "ref_pdb",
+            "ui:widget": "hidden"
+          },
+          "proteinFieldValue": {
+            "type": "string",
+            "value": "{protein_id}",
+            "ui:widget": "hidden"
+          }
+        },
+        "outputs": {
+          "outputs": { "type": "string" }
+        },
+        "results": ["Merged molecules"]
+      }
+    ]
+  }
+