fix: Protein and compound now checked against target

Author: Alan Christie

viewer/squonk_job_file_transfer.py

@@ -4,7 +4,7 @@
 import os
 import urllib.parse
 from pathlib import Path
-from typing import Dict, List, Tuple
+from typing import Any, Dict, List, Optional, Tuple
 
 from celery.utils.log import get_task_logger
 from django.conf import settings
@@ -100,7 +100,7 @@ def process_file_transfer(auth_token, job_transfer_id):
 
 def validate_file_transfer_files(
     request,
-) -> Tuple[Dict[str, str], List[Path], List[Path]]:
+) -> Tuple[Optional[Dict[str, str]], Optional[List[Path]], Optional[List[Path]]]:
     """Check the request and return a list of proteins and/or computed molecule file
     path references (paths relative to the media directory).
 
@@ -121,9 +121,9 @@ def validate_file_transfer_files(
         list of validated computed molecules (ComputedMolecule)
     """
 
-    logger.info('+ Validating file transfer files...')
+    target_id = request.data['target']
+    logger.info('+ Validating file transfer files ()...')
 
-    error: Dict[str, str] = {}
     protein_files: List[Path] = []
     compound_files: List[Path] = []
 
@@ -133,21 +133,24 @@ def validate_file_transfer_files(
             p.strip() for p in request.data['proteins'].split(',')
         ]
         for protein_path_and_file in protein_paths_and_files:
-            # It's a filename
             if protein_path_and_file.endswith('_apo-desolv.pdb'):
-                if SiteObservation.objects.filter(
-                    apo_desolv_file=protein_path_and_file
-                ).first():
+                if not (
+                    s_ob := SiteObservation.objects.filter(
+                        apo_desolv_file=protein_path_and_file
+                    ).first()
+                ):
+                    return tfr_validation_error(
+                        f'Unknown Protein: {protein_path_and_file}',
+                        status.HTTP_404_NOT_FOUND,
+                    )
+
+                if s_ob.experiment.experiment_upload.target.id == target_id:
                     protein_files.append(Path(protein_path_and_file))
                 else:
-                    error['message'] = f'Unknown Protein: {protein_path_and_file}'
-                    error['status'] = status.HTTP_404_NOT_FOUND
-                    return error, protein_files, compound_files
-
-        if not protein_files:
-            error['message'] = 'API expects a list of comma-separated protein codes'
-            error['status'] = status.HTTP_404_NOT_FOUND
-            return error, protein_files, compound_files
+                    return tfr_validation_error(
+                        f'Protein does not belong to Target: {protein_path_and_file}',
+                        status.HTTP_400_BAD_REQUEST,
+                    )
 
         logger.info(
             "+ Validated proteins (SiteObservations) [%d]",
@@ -159,36 +162,43 @@ def validate_file_transfer_files(
             p.strip() for p in request.data['compounds'].split(',')
         ]
         for compound_path_and_file in compound_paths_and_files:
-            if SiteObservation.objects.filter(
+            if not SiteObservation.objects.filter(
                 ligand_mol=compound_path_and_file
             ).first():
+                return tfr_validation_error(
+                    f'Unknown Compound: {compound_path_and_file}',
+                    status.HTTP_404_NOT_FOUND,
+                )
+
+            if s_ob.experiment.experiment_upload.target.id == target_id:
                 compound_files.append(Path(compound_path_and_file))
             else:
-                error['message'] = f'Unknown Compound: {compound_path_and_file}'
-                error['status'] = status.HTTP_404_NOT_FOUND
-                return error, protein_files, compound_files
-
-        if not compound_files:
-            error['message'] = 'API expects a list of comma-separated compound names'
-            error['status'] = status.HTTP_400_BAD_REQUEST
-            return error, protein_files, compound_files
+                return tfr_validation_error(
+                    f'Compound does not belong to Target: {compound_path_and_file}',
+                    status.HTTP_400_BAD_REQUEST,
+                )
 
         logger.info(
             "+ Validated compounds (SiteObservations) [%d]",
             len(compound_files),
         )
 
-    if protein_files or compound_files:
-        logger.info(
-            "- Validated file transfer files (%d, %d)",
-            len(protein_files),
-            len(compound_files),
+    if not protein_files and not compound_files:
+        return tfr_validation_error(
+            'A valid set of protein codes and/or a list of valid compound names must be provided',
+            status.HTTP_400_BAD_REQUEST,
         )
-        return error, protein_files, compound_files
 
-    error['message'] = (
-        'A valid set of protein codes and/or a list of valid'
-        ' compound names must be provided'
+    logger.info(
+        "- Validated file transfer files (%d, %d)",
+        len(protein_files),
+        len(compound_files),
     )
-    error['status'] = status.HTTP_400_BAD_REQUEST
-    return error, protein_files, compound_files
+    return None, protein_files, compound_files
+
+
+def tfr_validation_error(
+    error: str, status_code: int
+) -> Tuple[Dict[str, Any], None, None]:
+    """Returns the error and HTTP status code as a tuple for a response."""
+    return {'message': error, 'status': status_code}, None, None