Align 1247 with staging

.github/workflows/build-dev.yaml

@@ -85,12 +85,11 @@ jobs:
       with:
         context: .
         tags: ${{ steps.vars.outputs.BE_NAMESPACE }}/fragalysis-backend:${{ env.GITHUB_REF_SLUG }}
-    - name: Test
-      run: >
-        docker-compose -f docker-compose.test.yml up
-        --build
-        --exit-code-from tests
-        --abort-on-container-exit
+    - name: Test (docker compose)
+      uses: hoverkraft-tech/compose-action@v2.0.1
+      with:
+        compose-file: ./docker-compose.test.yml
+        up-flags: --build --exit-code-from tests --abort-on-container-exit
       env:
         BE_NAMESPACE: ${{ steps.vars.outputs.BE_NAMESPACE }}
         BE_IMAGE_TAG: ${{ env.GITHUB_REF_SLUG }}

.github/workflows/build-production.yaml

@@ -134,12 +134,11 @@ jobs:
         tags: |
           ${{ steps.vars.outputs.BE_NAMESPACE }}/fragalysis-backend:${{ steps.vars.outputs.tag }}
           ${{ steps.vars.outputs.BE_NAMESPACE }}/fragalysis-backend:stable
-    - name: Test
-      run: >
-        docker-compose -f docker-compose.test.yml up
-        --build
-        --exit-code-from tests
-        --abort-on-container-exit
+    - name: Test (docker compose)
+      uses: hoverkraft-tech/compose-action@v2.0.1
+      with:
+        compose-file: ./docker-compose.test.yml
+        up-flags: --build --exit-code-from tests --abort-on-container-exit
       env:
         BE_NAMESPACE: ${{ steps.vars.outputs.BE_NAMESPACE }}
         BE_IMAGE_TAG: ${{ steps.vars.outputs.tag }}

.github/workflows/build-staging.yaml

@@ -154,12 +154,11 @@ jobs:
       with:
         context: .
         tags: ${{ steps.vars.outputs.BE_NAMESPACE }}/fragalysis-backend:${{ steps.vars.outputs.tag }}
-    - name: Test
-      run: >
-        docker-compose -f docker-compose.test.yml up
-        --build
-        --exit-code-from tests
-        --abort-on-container-exit
+    - name: Test (docker compose)
+      uses: hoverkraft-tech/compose-action@v2.0.1
+      with:
+        compose-file: ./docker-compose.test.yml
+        up-flags: --build --exit-code-from tests --abort-on-container-exit
       env:
         BE_NAMESPACE: ${{ steps.vars.outputs.BE_NAMESPACE }}
         BE_IMAGE_TAG: ${{ steps.vars.outputs.tag }}

viewer/cset_upload.py

@@ -290,6 +290,19 @@ def create_mol(self, inchi, target, name=None) -> Compound:
                 current_identifier=name,
             )
             cpd.save()
+            # This is a new compound.
+            # We must now set relationships to the Proposal that it applies to.
+            # We do this by copying the relationships from the Target.
+            num_target_proposals = len(target.project_id.all())
+            assert num_target_proposals > 0
+            if num_target_proposals > 1:
+                logger.warning(
+                    'Compound Target %s has more than one Proposal (%d)',
+                    target.title,
+                    num_target_proposals,
+                )
+            for project in target.project_set.all():
+                cpd.project_id.add(project)
         except MultipleObjectsReturned as exc:
             # NB! when processing new uploads, Compound is always
             # fetched by inchi_key, so this shouldn't ever create
@@ -339,7 +352,6 @@ def set_mol(
         smiles = Chem.MolToSmiles(mol)
         inchi = Chem.inchi.MolToInchi(mol)
         molecule_name = mol.GetProp('_Name')
-        version = mol.GetProp('version')
 
         compound: Compound = self.create_mol(
             inchi, compound_set.target, name=molecule_name
@@ -449,8 +461,9 @@ def set_mol(
                     existing_computed_molecules.append(k)
 
         if len(existing_computed_molecules) == 1:
-            logger.info(
-                'Using existing ComputedMolecule %s', existing_computed_molecules[0]
+            logger.warning(
+                'Using existing ComputedMolecule %s and overwriting its metadata',
+                existing_computed_molecules[0],
             )
             computed_molecule = existing_computed_molecules[0]
         elif len(existing_computed_molecules) > 1:
@@ -485,7 +498,6 @@ def set_mol(
         computed_molecule.pdb = lhs_so
         # TODO: this is wrong
         computed_molecule.pdb_info = pdb_info
-        computed_molecule.version = version
         # Extract possible reference URL and Rationale
         # URLs have to be valid URLs and rationals must contain more than one word
         ref_url: Optional[str] = (

viewer/download_structures.py

@@ -104,6 +104,25 @@ def __init__(self, category):
         # fmt: on
 
 
+class UploadTagSubquery(Subquery):
+    """Annotate SiteObservation with tag of given category"""
+
+    def __init__(self, category):
+        # fmt: off
+        query = SiteObservationTag.objects.filter(
+            pk=Subquery(
+                SiteObvsSiteObservationTag.objects.filter(
+                    site_observation=OuterRef(OuterRef('pk')),
+                    site_obvs_tag__category=TagCategory.objects.get(
+                        category=category,
+                    ),
+                ).values('site_obvs_tag')[:1]
+            )
+        ).values('upload_name')[0:1]
+        super().__init__(query)
+        # fmt: on
+
+
 class CuratedTagSubquery(Exists):
     """Annotate SiteObservation with tag of given category"""
 
@@ -140,6 +159,10 @@ class ArchiveFile:
         'ligand_pdb': {},
         'ligand_mol': {},
         'ligand_smiles': {},
+        # additional ccp4 files, issue 1448
+        'event_file_crystallographic': {},
+        'diff_file_crystallographic': {},
+        'sigmaa_file_crystallographic': {},
     },
     'molecules': {
         'sdf_files': {},
@@ -423,14 +446,34 @@ def _metadata_file_zip(ziparchive, target, site_observations):
     logger.info('+ Processing metadata')
 
     annotations = {}
-    values = ['code', 'longcode', 'cmpd__compound_code', 'smiles', 'downloaded']
-    header = ['Code', 'Long code', 'Compound code', 'Smiles', 'Downloaded']
+    values = [
+        'code',
+        'longcode',
+        'experiment__code',
+        'cmpd__compound_code',
+        'smiles',
+        'canon_site_conf__canon_site__centroid_res',
+        'downloaded',
+    ]
+    header = [
+        'Code',
+        'Long code',
+        'Experiment code',
+        'Compound code',
+        'Smiles',
+        'Centroid res',
+        'Downloaded',
+    ]
 
     for category in TagCategory.objects.filter(category__in=TAG_CATEGORIES):
         tag = f'tag_{category.category.lower()}'
+        upload_tag = f'upload_tag_{category.category.lower()}'
         values.append(tag)
-        header.append(category.category)
+        header.append(f'{category.category} alias')
         annotations[tag] = TagSubquery(category.category)
+        values.append(upload_tag)
+        header.append(f'{category.category} upload name')
+        annotations[upload_tag] = UploadTagSubquery(category.category)
 
     pattern = re.compile(r'\W+')  # non-alphanumeric characters
     for tag in SiteObservationTag.objects.filter(
@@ -812,6 +855,7 @@ def _create_structures_dict(site_obvs, protein_params, other_params):
                             )
                         )
                     else:
+                        # file not in upload
                         archive_path = str(apath.joinpath(param))
 
                     afile = [
@@ -820,12 +864,38 @@ def _create_structures_dict(site_obvs, protein_params, other_params):
                             archive_path=archive_path,
                         )
                     ]
+
                 else:
                     logger.warning('Unexpected param: %s', param)
                     continue
 
                 zip_contents['proteins'][param][so.code] = afile
 
+                # add additional ccp4 files (issue 1448)
+                ccps = ('sigmaa_file', 'diff_file', 'event_file')
+                if param in ccps:
+                    # these only come from siteobservation object
+                    model_attr = getattr(so, param)
+                    if model_attr and model_attr != 'None':
+                        apath = Path('aligned_files').joinpath(so.code)
+                        ccp_path = Path(model_attr.name)
+                        path = ccp_path.parent.joinpath(
+                            f'{ccp_path.stem}_crystallographic{ccp_path.suffix}'
+                        )
+                        archive_path = str(
+                            apath.joinpath(path.parts[-1].replace(so.longcode, so.code))
+                        )
+
+                        afile = [
+                            ArchiveFile(
+                                path=str(path),
+                                archive_path=archive_path,
+                            )
+                        ]
+                        zip_contents['proteins'][f'{param}_crystallographic'][
+                            so.code
+                        ] = afile
+
     zip_contents['molecules']['single_sdf_file'] = other_params['single_sdf_file']
     zip_contents['molecules']['sdf_info'] = other_params['sdf_info']
 

viewer/migrations/0059_remove_computedmolecule_version.py

@@ -0,0 +1,17 @@
+# Generated by Django 3.2.25 on 2024-07-10 08:31
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0058_auto_20240614_1016'),
+    ]
+
+    operations = [
+        migrations.RemoveField(
+            model_name='computedmolecule',
+            name='version',
+        ),
+    ]

viewer/migrations/0060_canonsite_centroid_res.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.2.25 on 2024-07-29 12:50
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('viewer', '0059_remove_computedmolecule_version'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='canonsite',
+            name='centroid_res',
+            field=models.TextField(null=True),
+        ),
+    ]

viewer/models.py

@@ -396,6 +396,7 @@ class CanonSite(Versionable, models.Model):
     canon_site_num = models.IntegerField(
         null=True, help_text="numeric canon site id (enumerated on creation)"
     )
+    centroid_res = models.TextField(null=True)
 
     objects = models.Manager()
     filter_manager = CanonSiteDataManager()
@@ -1027,7 +1028,6 @@ class ComputedMolecule(models.Model):
         max_length=255,
         help_text="Link to pdb file; user-uploaded pdb or pdb.experiment.pdb_info",
     )
-    version = models.PositiveSmallIntegerField(null=False, default=1)
 
     def __str__(self) -> str:
         return f"{self.smiles}"