Merge pull request #528 from xchem/m2ms-1334-short-code-prefix

Short code prefix and tooltip read from yaml file (issue 1334)

viewer/managers.py

@@ -17,6 +17,7 @@ def filter_qs(self):
         ).annotate(
             target=F("experiment__experiment_upload__target"),
             compound_code=F("cmpd__compound_code"),
+            prefix_tooltip=F("experiment__prefix_tooltip"),
         )
 
         return qs

viewer/migrations/0043_experiment_prefix_tooltip.py

@@ -0,0 +1,17 @@
+# Generated by Django 3.2.23 on 2024-02-13 15:12
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('viewer', '0042_alter_xtalformsite_xtalform_site_num'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='experiment',
+            name='prefix_tooltip',
+            field=models.TextField(null=True),
+        ),
+    ]

viewer/models.py

@@ -196,6 +196,7 @@ class Experiment(models.Model):
     map_info = ArrayField(models.FileField(max_length=255), null=True)
     type = models.PositiveSmallIntegerField(null=True)
     pdb_sha256 = models.TextField(null=True)
+    prefix_tooltip = models.TextField(null=True)
     compounds = models.ManyToManyField(
         "Compound",
         through="ExperimentCompound",

viewer/serializers.py

@@ -951,6 +951,7 @@ class Meta:
 
 class SiteObservationReadSerializer(serializers.ModelSerializer):
     compound_code = serializers.StringRelatedField()
+    prefix_tooltip = serializers.StringRelatedField()
 
     class Meta:
         model = models.SiteObservation

viewer/target_loader.py

@@ -700,6 +700,7 @@ def _enumerate_objects(self, objects: dict, attr: str) -> None:
     def process_experiment(
         self,
         item_data: tuple[str, dict] | None = None,
+        prefix_tooltips: dict[str, str] | None = None,
         validate_files: bool = True,
         **kwargs,
     ) -> ProcessedObject | None:
@@ -734,6 +735,7 @@ def process_experiment(
         """
         del kwargs
         assert item_data
+        assert prefix_tooltips
         logger.debug("incoming data: %s", item_data)
         experiment_name, data = item_data
 
@@ -813,6 +815,9 @@ def process_experiment(
         # version	int	old versions are kept	target loader
         version = 1
 
+        code_prefix = extract(key="code_prefix")
+        prefix_tooltip = prefix_tooltips.get(code_prefix, "")
+
         fields = {
             "code": experiment_name,
         }
@@ -830,6 +835,7 @@ def process_experiment(
             "mtz_info": str(self._get_final_path(mtz_info)),
             "cif_info": str(self._get_final_path(cif_info)),
             "map_info": map_info_paths,
+            "prefix_tooltip": prefix_tooltip,
             # this doesn't seem to be present
             # pdb_sha256:
         }
@@ -839,6 +845,7 @@ def process_experiment(
         index_fields = {
             "xtalform": assigned_xtalform,
             "smiles": smiles,
+            "code_prefix": code_prefix,
         }
 
         return ProcessedObject(
@@ -1437,7 +1444,6 @@ def process_bundle(self):
             self.report.log(logging.ERROR, msg)
             raise KeyError(msg) from exc
 
-        # moved this bit from init
         self.target, target_created = Target.objects.get_or_create(
             title=self.target_name,
             display_name=self.target_name,
@@ -1475,6 +1481,7 @@ def process_bundle(self):
         self.version_number = meta["version_number"]
         self.version_dir = meta["version_dir"]
         self.previous_version_dirs = meta["previous_version_dirs"]
+        prefix_tooltips = meta["code_prefix_tooltips"]
 
         # check transformation matrix files
         (  # pylint: disable=unbalanced-tuple-unpacking
@@ -1533,7 +1540,9 @@ def process_bundle(self):
             ),
         )
 
-        experiment_objects = self.process_experiment(yaml_data=crystals)
+        experiment_objects = self.process_experiment(
+            yaml_data=crystals, prefix_tooltips=prefix_tooltips
+        )
         compound_objects = self.process_compound(
             yaml_data=crystals, experiments=experiment_objects
         )
@@ -1643,16 +1652,14 @@ def process_bundle(self):
             canon_site_confs=canon_site_conf_objects,
         )
 
-        values = ["xtalform_site__xtalform", "canon_site_conf__canon_site", "cmpd"]
+        # values = ["canon_site_conf__canon_site", "cmpd"]
+        values = ["experiment"]
         qs = (
             SiteObservation.objects.values(*values)
             .order_by(*values)
             .annotate(obvs=ArrayAgg("id"))
             .values_list("obvs", flat=True)
         )
-        current_list = SiteObservation.objects.filter(
-            experiment__experiment_upload__target=self.target
-        ).values_list('code', flat=True)
         for elem in qs:
             # objects in this group should be named with same scheme
             so_group = SiteObservation.objects.filter(pk__in=elem)
@@ -1681,20 +1688,27 @@ def process_bundle(self):
                     # technically it should be validated in previous try-catch block
                     logger.error("Non-standard SiteObservation code 2: %s", last)
 
-            logger.debug("iter_pos: %s", iter_pos)
-
             # ... and create new one starting from next item
             suffix = alphanumerator(start_from=iter_pos)
             for so in so_group.filter(code__isnull=True):
-                code = f"{so.experiment.code.split('-')[1]}{next(suffix)}"
+                code_prefix = experiment_objects[so.experiment.code].index_data[
+                    "code_prefix"
+                ]
+                code = f"{code_prefix}{so.experiment.code.split('-')[1]}{next(suffix)}"
 
                 # test uniqueness for target
                 # TODO: this should ideally be solved by db engine, before
                 # rushing to write the trigger, have think about the
                 # loader concurrency situations
-                prefix = alphanumerator()
-                while code in current_list:
-                    code = f"{next(prefix)}{code}"
+                if SiteObservation.objects.filter(
+                    experiment__experiment_upload__target=self.target,
+                    code=code,
+                ).exists():
+                    msg = (
+                        f"short code {code} already exists for this target;  "
+                        + "specify a code_prefix to resolve this conflict"
+                    )
+                    self.report.log(logging.ERROR, msg)
 
                 so.code = code
                 so.save()