clinicedc 2.0.23__py3-none-any.whl → 2.0.24__py3-none-any.whl

{clinicedc-2.0.23.dist-info → clinicedc-2.0.24.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clinicedc
-Version: 2.0.23
+Version: 2.0.24
 Summary: A clinical trials data management framework built on Django
 Keywords: django,clinicedc,edc,clinical trials,research,data management,esource
 Author: Erik van Widenfelt, Jonathan Willitts

{clinicedc-2.0.23.dist-info → clinicedc-2.0.24.dist-info}/RECORD

@@ -2793,11 +2793,11 @@ edc_randomization/model_mixins.py,sha256=pKLkZJeYgobKPyHVJTby8Q7zBKQoflbLgraTN4p
 edc_randomization/models/__init__.py,sha256=iaJ6FM7VVqLpp8M-OjVWjohp4ELdxtPXqbEiT3iN5Tw,94
 edc_randomization/models/edc_permissions.py,sha256=f6P4zXxLQdTAbn2KnFlwfE86Lmzj7Ecp4JJ2F8mrwTc,286
 edc_randomization/models/randomization_list.py,sha256=Hd5yUSZ5HBKhNzYdlbJufab8U2x3Dzw8n4WXnYzJxyc,253
-edc_randomization/randomization_list_importer.py,sha256=v8d1klIfAsf9CwR_4HLLzifDnJvFD2bXhDOe0XqznjM,12366
-edc_randomization/randomization_list_verifier.py,sha256=0JqlbVCBZzx18Vxp2gID4zHjZMyO1LaHzqe4zTzRUpY,6481
+edc_randomization/randomization_list_importer.py,sha256=9jIJTG7rGjze4WmaFsJaw4qhFvy5mugZ4mx1CKKV6_o,12416
+edc_randomization/randomization_list_verifier.py,sha256=b9-ZbaWSSv6fCrrDgHjijUACTMsUuU_htbkHqAcE8l4,6669
 edc_randomization/randomizer.py,sha256=N57PvCGjsjlw4r4V-zE5K7uWnLUw4QwZREu-mQ-O_4U,12939
 edc_randomization/randomizers.py,sha256=JvMDAnsgvRZkl50Bawm2iLsyw3bfWfGwBafn54K5g44,297
-edc_randomization/site_randomizers.py,sha256=T6u1cNPZtoh5ajdsBciSVWzZYZyOPbiTqS9VBGKJ7H8,4077
+edc_randomization/site_randomizers.py,sha256=et5Yf92ld8qgn-AThrBTRALB3WInI03UK4yGw2PlsKo,4499
 edc_randomization/system_checks.py,sha256=S_2Vkq3J3DQVEXOV3JNNlCzuZcl1l34-tTnaBaSZaBk,3025
 edc_randomization/urls.py,sha256=yQnOoy5U5uL00f7_JJcZk7toskmZunG_kJdl-epCV9U,223
 edc_randomization/utils.py,sha256=uRTtoyAuWo5D6y65ZHBWMSody8IMJBK6cS3mFmJGIMw,5730
@@ -3406,7 +3406,7 @@ edc_vitals/models/fields/waist_circumference.py,sha256=fZcHFDdEwWLjIVLktKrFCD9UU
 edc_vitals/models/fields/weight.py,sha256=zo9_9e3Cpu0UqoRbWS-iDkcDo6fK80b1dDQy4x4MyxE,921
 edc_vitals/utils.py,sha256=vXid44KUXxeaSyund_y5MNXc5DFJs052_PwUAjszE2k,1384
 edc_vitals/validators.py,sha256=vNiElWMs0rRnHRNuVoPLRf0rW_C_0xcfUyep1Y_Si5s,156
-clinicedc-2.0.23.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-clinicedc-2.0.23.dist-info/WHEEL,sha256=-neZj6nU9KAMg2CnCY6T3w8J53nx1kFGw_9HfoSzM60,79
-clinicedc-2.0.23.dist-info/METADATA,sha256=E4Mthvgcki8gT3t1mDJIiAyqCER0KsawkYqC0hkWsSI,15787
-clinicedc-2.0.23.dist-info/RECORD,,
+clinicedc-2.0.24.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+clinicedc-2.0.24.dist-info/WHEEL,sha256=-neZj6nU9KAMg2CnCY6T3w8J53nx1kFGw_9HfoSzM60,79
+clinicedc-2.0.24.dist-info/METADATA,sha256=SanRpzDjK5JhHNRsmoNLCYZtF9Q9k3bXXX2CdYsZ7ME,15787
+clinicedc-2.0.24.dist-info/RECORD,,

edc_randomization/randomization_list_importer.py

@@ -55,13 +55,13 @@ class RandomizationListImporter:
 
 
     Format:
-        sid,assignment,site_name, orig_site, orig_allocation, orig_desc
-        1,single_dose,gaborone
-        2,two_doses,gaborone
+        sid,site_name, assignment, description, orig_site, orig_allocation, orig_desc
+        1,gaborone,intervention,single_dose
+        2,gaborone,control,two_doses
         ...
     """
 
-    required_csv_fieldnames = ["sid", "assignment", "site_name"]
+    required_csv_fieldnames = ("sid", "assignment", "site_name", "description")
     verifier_cls = RandomizationListVerifier
 
     def __init__(

edc_randomization/randomization_list_verifier.py

@@ -31,7 +31,7 @@ class RandomizationListVerifier:
         fieldnames=None,
         sid_count_for_tests=None,
         required_csv_fieldnames: list[str] | None = None,
-        **kwargs,
+        **kwargs,  # noqa: ARG002
     ):
         self.count: int = 0
         self.messages: list[str] = []
@@ -68,33 +68,38 @@ class RandomizationListVerifier:
                 )
             elif message := self.verify():
                 self.messages.append(message)
-        if self.messages:
-            if (
-                "migrate" not in sys.argv
-                and "makemigrations" not in sys.argv
-                and "import_randomization_list" not in sys.argv
-            ):
-                raise RandomizationListError(", ".join(self.messages))
+        if self.messages and (
+            "migrate" not in sys.argv
+            and "makemigrations" not in sys.argv
+            and "import_randomization_list" not in sys.argv
+        ):
+            raise RandomizationListError(", ".join(self.messages))
 
     def verify(self) -> str | None:
         message = None
+
         with self.randomizationlist_path.open(mode="r") as f:
             reader = csv.DictReader(f)
-            for index, row in enumerate(reader, start=1):
-                row = {k: v.strip() for k, v in row.items() if k}
-                message = self.inspect_row(index - 1, row)
-                if message:
-                    break
-                if self.sid_count_for_tests and index == self.sid_count_for_tests:
-                    break
-        if not message:
-            if self.count != index:
-                message = (
-                    f"Randomization list count is off. Expected {index} (CSV). "
-                    f"Got {self.count} (model_cls). See file "
-                    f"{self.randomizationlist_path}. "
-                    f"Resolve this issue before using the system."
-                )
+            all_rows = [{k: v.strip() for k, v in row.items() if k} for row in reader]
+            sorted_rows = sorted(
+                all_rows, key=lambda row: (row.get("site_name", ""), row.get("sid", ""))
+            )
+
+        for index, row in enumerate(sorted_rows, start=1):
+            sys.stdout.write(f"Index: {index}, SID: {row.get('sid')}, Row: {row}\n")
+            message = self.inspect_row(index - 1, row)
+            if message:
+                break
+            if self.sid_count_for_tests and index == self.sid_count_for_tests:
+                break
+
+        if not message and self.count != index:
+            message = (
+                f"Randomization list count is off. Expected {index} (CSV). "
+                f"Got {self.count} (model_cls). See file "
+                f"{self.randomizationlist_path}. "
+                f"Resolve this issue before using the system."
+            )
         return message
 
     def inspect_row(self, index: int, row) -> str | None:
@@ -103,7 +108,7 @@ class RandomizationListVerifier:
         Note:Index is zero-based
         """
         message = None
-        obj1 = self.randomizer_model_cls.objects.all().order_by("sid")[index]
+        obj1 = self.randomizer_model_cls.objects.all().order_by("site_name", "sid")[index]
         try:
             obj2 = self.randomizer_model_cls.objects.get(sid=row["sid"])
         except ObjectDoesNotExist:

edc_randomization/site_randomizers.py

@@ -28,7 +28,22 @@ class SiteRandomizerError(Exception):
 
 
 class SiteRandomizers:
-    """Main controller of :class:`SiteRandomizers` objects."""
+    """Main controller of :class:`SiteRandomizers` objects.
+
+    To rescan the CSV file for randomizer additional slots:
+
+        from edc_randomization.site_randomizers import site_randomizers
+        # assuming the randimizer is "default"
+        site_randomizers.get("default").import_list(add=True,dryrun=True)
+
+    If all OK:
+
+        # assuming the randimizer is "default"
+        site_randomizers.get("default").import_list(add=True,dryrun=False)
+
+    See
+
+    """
 
     def __init__(self):
         self._registry = {}
@@ -57,12 +72,12 @@ class SiteRandomizers:
     def get(self, name):
         try:
             return self._registry[str(name)]
-        except KeyError:
+        except KeyError as e:
             raise NotRegistered(
                 f"A Randomizer class by this name is not registered. "
                 f"Expected one of {list(self._registry.keys())}. "
                 f"Got '{name}'. See site_randomizer."
-            )
+            ) from e
 
     def get_by_model(self, model=None):
         """Returns the randomizer class for this model label_lower.
@@ -75,10 +90,12 @@ class SiteRandomizers:
         return None
 
     def get_as_choices(self):
-        choices = []
-        for randomizer_cls in self._registry.values():
-            choices.append((randomizer_cls.name, randomizer_cls.name))
-        return tuple(choices)
+        return tuple(
+            [
+                (randomizer_cls.name, randomizer_cls.name)
+                for randomizer_cls in self._registry.values()
+            ]
+        )
 
     def randomize(
         self,
@@ -115,7 +132,7 @@ class SiteRandomizers:
                         before_import_registry = copy.copy(site_randomizers._registry)
                         import_module(f"{app}.{module_name}")
                         if verbose:
-                            sys.stdout.write(" * registered randomizer from " f"'{app}'\n")
+                            sys.stdout.write(f" * registered randomizer from '{app}'\n")
                     except Exception as e:
                         if f"No module named '{app}.{module_name}'" not in str(e):
                             raise