clinicedc 2.0.16__py3-none-any.whl → 2.0.18__py3-none-any.whl

{clinicedc-2.0.16.dist-info → clinicedc-2.0.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clinicedc
-Version: 2.0.16
+Version: 2.0.18
 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-2.0.16.dist-info → clinicedc-2.0.18.dist-info}/RECORD

@@ -1963,11 +1963,11 @@ edc_model_form/mixins/inline_model_form_mixin.py,sha256=dxpzFcwHoNi2y7vWF1QdAqOb
 edc_model_form/mixins/report_datetime_modelform_mixin.py,sha256=f1DrM-aUh2o3DM65MM3nwiZUXhhnvth8_3tvbS1cWOQ,1008
 edc_model_form/urls.py,sha256=_sVCnQeiAFRYKhxga3_DjoKj_4bgs1s2gjcynDiapvA,111
 edc_model_form/utils.py,sha256=gGe3etrp5YF4AKMGFIR3I9V1CfX4c5Wm6fK-8JkUeT4,538
-edc_model_to_dataframe/__init__.py,sha256=iDR_F5oKkKDL9FfBXl0WKpwc2iOWbOlY-8wpCipBNnQ,115
+edc_model_to_dataframe/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 edc_model_to_dataframe/apps.py,sha256=US1ehhJPgkvmIDZXiUPMoSjHTWIztUbYGtx_azTXPIQ,290
 edc_model_to_dataframe/constants.py,sha256=xgCr2ZXUsjZqf4wfpY0JBhQoARzQEVS8tnkfBWwOMVQ,702
-edc_model_to_dataframe/model_to_dataframe.py,sha256=DDuDIEpgEHjTTrqcjdYMLERvFl9h-HHhxYaapFepO9U,18829
-edc_model_to_dataframe/read_frame_edc.py,sha256=D3Bai4ce4u6942OU8sad1OEAeDRIT1DQxYOQib5AMDE,791
+edc_model_to_dataframe/model_to_dataframe.py,sha256=cOTcoe9ivJERAXt3dULtoon6j9_cgh2-T-y3P0FBimo,18493
+edc_model_to_dataframe/read_frame_edc.py,sha256=UNe2f5bJi1Wkn4Jyva5TMnhyxk8vvGpG4U12kGyqqVY,820
 edc_model_to_dataframe/urls.py,sha256=KChLHeE6yfONC6IdMm3Q4U3u7tmy_Mb1w2lrbpFz96g,148
 edc_navbar/__init__.py,sha256=Y95juevvOawGZmOV3Ofef7oGwYSWWttAYT0v0mehkJc,195
 edc_navbar/apps.py,sha256=fiWHsCYaDnHXNfYUu6DuvlAcO2k45-zkdbuXwXI3ksc,367
@@ -2133,7 +2133,7 @@ edc_pdutils/constants.py,sha256=v4J4xjBJC49IeLQqVrjZyqF1OKAzOjm-TMqF38siR6g,785
 edc_pdutils/database.py,sha256=bevHPm0BDsMai6tfR94nERV3bIOQz4pkoniGYp0Ha3s,4468
 edc_pdutils/dataframes/__init__.py,sha256=mr2vvMm1E5sj5VXbk3iUKlZy2HeS3odZlQyi5HhiiEU,264
 edc_pdutils/dataframes/get_appointments.py,sha256=R3lzLbloR-pabMXREhcgmrfMC1CP6d6DrnxNyLbTOQI,2503
-edc_pdutils/dataframes/get_crf.py,sha256=3y9R6squz1eza0OWiAdaNVEIdBO_2QhB1-9br97NC_s,4453
+edc_pdutils/dataframes/get_crf.py,sha256=WVRs9VHTpaYBRAXvbWeoDGNGPqe096vUp0hegZPEFyc,4468
 edc_pdutils/dataframes/get_eos.py,sha256=qzlERHSm-vydI8M4XuSF5oIIcBtYbu7PxKXWXb5wikQ,1350
 edc_pdutils/dataframes/get_next_appointments.py,sha256=VUuTQ5T15PxAVNlJId2rH70PyAzaHXqFGWJH0qd4Kfs,784
 edc_pdutils/dataframes/get_subject_consent.py,sha256=e-G4rCdRtv2c9dBDA6HsezoZgxj8DPtyktnc5b6Mvj0,2030
@@ -2142,7 +2142,7 @@ edc_pdutils/df_exporters/__init__.py,sha256=K2CbrO9yrBEr_9k6nRbSOepBhBWY1tCcHCd_
 edc_pdutils/df_exporters/csv_crf_inline_tables_exporter.py,sha256=OUV6BGVFgYXQ3osccPVqAZ_2hRbfQew86BLqFkuEFS8,3218
 edc_pdutils/df_exporters/csv_crf_tables_exporter.py,sha256=hBx5n-Khr9ooO_RfTtEUjyDx6JL0QuNCmFpFDI7azXY,1047
 edc_pdutils/df_exporters/csv_exporter.py,sha256=1JE9DGWKIfA1iTXywz9gVytW1aP7Ebfj3k7Mt5qvw2k,10029
-edc_pdutils/df_exporters/csv_model_exporter.py,sha256=rUaAuSHugLZQEFmVSzoIUjszeFYeTxUZAZWUsawxon0,1567
+edc_pdutils/df_exporters/csv_model_exporter.py,sha256=7HJvtsgIuC5EgGyEc_YLE3cEHim-I-Na4UKZy0_9sZw,1586
 edc_pdutils/df_exporters/csv_noncrf_tables_exporter.py,sha256=twgj1hM53KgiqbHoV1m54eEuZ6-I6BWdJcwNLmoefiY,788
 edc_pdutils/df_exporters/tables_exporter.py,sha256=4juRZ87xl7Ph6NzC-iss2pcyq1muLmhezgz6IpkYP7g,4576
 edc_pdutils/df_handlers/__init__.py,sha256=8c3N4G_fmc_6bshSjAtEu-aQelGzN4ZeXU7J6s0lfRo,123
@@ -2157,7 +2157,7 @@ edc_pdutils/dialects/rs_dialect.py,sha256=G1aGOeefsJj5f0souyoJBBQ-AXHyli0Gxqeib6
 edc_pdutils/helper.py,sha256=dRujtvFA1pbuPoFjJ5M2ElAdA1j5qMbfGMspg1weD5k,1667
 edc_pdutils/management/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 edc_pdutils/management/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-edc_pdutils/management/commands/export_models.py,sha256=hLatz0dSvRAzlTe_qNwIElYwOuWiwJd8lAZpjDsBNQw,9554
+edc_pdutils/management/commands/export_models.py,sha256=ALBuoBv0rSmXw8FSIabkkZer7Y_rQvXqVYUmnQS704s,9573
 edc_pdutils/mappings.py,sha256=qlUrcoQdHg5vCEizEwF6EByqJedmYDVT6r94QDEi-Hg,77
 edc_pdutils/migrations/0001_initial.py,sha256=yZ8Ap-c1W87E-Bud74X8BAcbqgjWKQsOl3WykJRz3Xw,12271
 edc_pdutils/migrations/0002_auto_20180921_2242.py,sha256=J2gDXyF7AnHZiZUTDp4CsnGl87QGdu4t8vTW34Ww4Bs,548
@@ -2186,7 +2186,7 @@ edc_pdutils/utils/datetime_to_date.py,sha256=VQd6BVHxB6c0l5LT19j0-R5so3gVtEB_xFC
 edc_pdutils/utils/decrypt.py,sha256=zZhcnOkpgngoO_YEJZHFllFlLLnt8w2fRsqDFMirI9g,652
 edc_pdutils/utils/get_export_folder.py,sha256=l95sw3PGf2Sw_tFWNAkRvcZf5PDwUhqiCHeXBbCnvUU,260
 edc_pdutils/utils/identity256.py,sha256=3o5nAx8bKPPfi3zuFVsdYMP2VMygIKUJ7_7L6-i3wPo,717
-edc_pdutils/utils/missing_subject_identifiers.py,sha256=UGWdg9Mr1xvsEgq0jUx7sX3oK26fN1zDfTNCYw1-lZI,1811
+edc_pdutils/utils/missing_subject_identifiers.py,sha256=fzEa-U76st6EB7c2bf3YqQpIL3FuLvOpn_Ht-DP3hoE,1830
 edc_pdutils/utils/model_from_table_name.py,sha256=ahR04BOxoKxOPMob58fSH7gj3CNbrRMK_j8bC1xggUE,167
 edc_pdutils/utils/refresh_model_from_dataframe.py,sha256=Ct6sYEt7zOMm0jC23StpzLSbaStbzLP8SX3dTIOryZE,543
 edc_pdutils/utils/table_names.py,sha256=T8gXHN5ALXxshRP23nC3unzwIamLQRi7iQezBZvn1eA,1869
@@ -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-2.0.16.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-clinicedc-2.0.16.dist-info/WHEEL,sha256=-neZj6nU9KAMg2CnCY6T3w8J53nx1kFGw_9HfoSzM60,79
-clinicedc-2.0.16.dist-info/METADATA,sha256=yACQMEfCdkmBMoz9yz7R4jaTs-ToDfcahB4QqGBUqII,15899
-clinicedc-2.0.16.dist-info/RECORD,,
+clinicedc-2.0.18.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+clinicedc-2.0.18.dist-info/WHEEL,sha256=-neZj6nU9KAMg2CnCY6T3w8J53nx1kFGw_9HfoSzM60,79
+clinicedc-2.0.18.dist-info/METADATA,sha256=7nXGZliVuraX2Qnysh6GdRt_PFSZ3A-6bFDx6AyR538,15899
+clinicedc-2.0.18.dist-info/RECORD,,

edc_model_to_dataframe/__init__.py

@@ -1,2 +0,0 @@
-from .model_to_dataframe import ModelToDataframe, ModelToDataframeError
-from .read_frame_edc import read_frame_edc

edc_model_to_dataframe/model_to_dataframe.py

@@ -1,28 +1,23 @@
 from __future__ import annotations
 
+import contextlib
 from copy import copy
-from typing import TYPE_CHECKING
 
 import numpy as np
 import pandas as pd
 from django.apps import apps as django_apps
+from django.contrib.sites.models import Site
 from django.core.exceptions import FieldError
 from django.db import OperationalError
+from django.db.models import QuerySet
 from django_crypto_fields.utils import get_encrypted_fields, has_encrypted_fields
 from django_pandas.io import read_frame
+from pandas import Series
 
-from .constants import ACTION_ITEM_COLUMNS, SYSTEM_COLUMNS
-
-if TYPE_CHECKING:
-    from django.db.models import QuerySet
-
-    from edc_model.models import BaseUuidModel
-    from edc_sites.model_mixins import SiteModelMixin
-
-    class MyModel(SiteModelMixin, BaseUuidModel):
-        class Meta(BaseUuidModel.Meta):
-            pass
+from edc_lab.models import Panel
+from edc_list_data.model_mixins import ListModelMixin, ListUuidModelMixin
 
+from .constants import ACTION_ITEM_COLUMNS, SYSTEM_COLUMNS
 
 __all__ = ["ModelToDataframe", "ModelToDataframeError"]
 
@@ -52,16 +47,16 @@ class ModelToDataframe:
     See also: get_crf()
     """
 
-    sys_field_names: list[str] = [
+    sys_field_names: tuple[str, ...] = (
         "_state",
         "_user_container_instance",
         "_domain_cache",
         "using",
         "slug",
-    ]
-    edc_sys_columns: list[str] = SYSTEM_COLUMNS
-    action_item_columns: list[str] = ACTION_ITEM_COLUMNS
-    illegal_chars: dict[str] = {
+    )
+    edc_sys_columns: tuple[str, ...] = SYSTEM_COLUMNS
+    action_item_columns: tuple[str, ...] = ACTION_ITEM_COLUMNS
+    illegal_chars: dict[str, str] = {  # noqa: RUF012
         "\u2019": "'",
         "\u2018": "'",
         "\u201d": '"',
@@ -72,7 +67,7 @@ class ModelToDataframe:
     def __init__(
         self,
         model: str | None = None,
-        queryset: QuerySet | None = None,
+        queryset: [QuerySet] | None = None,
         query_filter: dict | None = None,
         decrypt: bool | None = None,
         drop_sys_columns: bool | None = None,
@@ -104,7 +99,7 @@ class ModelToDataframe:
         try:
             self.model_cls = django_apps.get_model(self.model)
         except LookupError as e:
-            raise LookupError(f"Model is {self.model}. Got `{e}`")
+            raise LookupError(f"Model is {self.model}. Got `{e}`") from e
         if self.sites:
             try:
                 if queryset:
@@ -151,7 +146,7 @@ class ModelToDataframe:
 
             dataframe = self.merge_m2ms(dataframe)
 
-            dataframe.rename(columns=self.columns, inplace=True)
+            dataframe = dataframe.rename(columns=self.columns)
 
             # remove timezone if asked
             if self.remove_timezone:
@@ -174,12 +169,12 @@ class ModelToDataframe:
                 dataframe[column] = dataframe[column].dt.total_seconds()
 
             # fillna
-            dataframe.fillna(value=np.nan, axis=0, inplace=True)
+            dataframe = dataframe.fillna(value=np.nan, axis=0)
 
             # remove illegal chars
             for column in list(dataframe.select_dtypes(include=["object"]).columns):
                 dataframe[column] = dataframe.apply(
-                    lambda x: self._clean_chars(x[column]), axis=1
+                    lambda x, col=column: self._clean_chars(x[col]), axis=1
                 )
             self._dataframe = dataframe
         return self._dataframe
@@ -188,7 +183,7 @@ class ModelToDataframe:
         queryset = self.queryset.values_list(*self.columns).filter(**self.query_filter)
         return pd.DataFrame(list(queryset), columns=[v for v in self.columns])
 
-    def get_dataframe_with_encrypted_fields(self, row_count: int) -> pd.DataFrame:
+    def get_dataframe_with_encrypted_fields(self, row_count: int) -> pd.DataFrame:  # noqa: ARG002
         df = read_frame(
             self.queryset.filter(**self.query_filter), verbose=self.read_frame_verbose
         )
@@ -233,28 +228,27 @@ class ModelToDataframe:
             dataframe = dataframe.merge(df_m2m, on="id", how="left")
         return dataframe
 
-    def _clean_chars(self, s):
-        try:
-            s = s if s else s
-        except ValueError:
-            pass
-        else:
-            if s:
-                for k, v in self.illegal_chars.items():
-                    try:
-                        s = s.replace(k, v)
-                    except (AttributeError, TypeError):
-                        break
-        return s
+    def _clean_chars(self, s: Series) -> Series:
+        if not s.empty:
+            for k, v in self.illegal_chars.items():
+                try:
+                    s = s.replace(k, v)
+                except (AttributeError, TypeError):
+                    break
+            return s
+        return np.nan
 
     def move_sys_columns_to_end(self, columns: dict[str, str]) -> dict[str, str]:
         system_columns = [
             f.name for f in self.model_cls._meta.get_fields() if f.name in SYSTEM_COLUMNS
         ]
         new_columns = {k: v for k, v in columns.items() if k not in system_columns}
-        if system_columns:
-            if len(new_columns.keys()) != len(columns.keys()) and not self.drop_sys_columns:
-                new_columns.update({k: k for k in system_columns})
+        if (
+            system_columns
+            and len(new_columns.keys()) != len(columns.keys())
+            and not self.drop_sys_columns
+        ):
+            new_columns.update({k: k for k in system_columns})
         return new_columns
 
     def move_action_item_columns(self, columns: dict[str, str]) -> dict[str, str]:
@@ -262,12 +256,11 @@ class ModelToDataframe:
             f.name for f in self.model_cls._meta.get_fields() if f.name in ACTION_ITEM_COLUMNS
         ]
         new_columns = {k: v for k, v in columns.items() if k not in ACTION_ITEM_COLUMNS}
-        if action_item_columns:
-            if (
-                len(new_columns.keys()) != len(columns.keys())
-                and not self.drop_action_item_columns
-            ):
-                new_columns.update({k: k for k in ACTION_ITEM_COLUMNS})
+        if action_item_columns and (
+            len(new_columns.keys()) != len(columns.keys())
+            and not self.drop_action_item_columns
+        ):
+            new_columns.update({k: k for k in ACTION_ITEM_COLUMNS})
         return new_columns
 
     @property
@@ -285,12 +278,10 @@ class ModelToDataframe:
             columns = {col: col for col in columns_list}
             for column_name in columns_list:
                 if column_name.endswith("_visit_id"):
-                    try:
+                    with contextlib.suppress(FieldError):
                         columns = self.add_columns_for_subject_visit(
                             column_name=column_name, columns=columns
                         )
-                    except FieldError:
-                        pass
                 if column_name.endswith("_requisition") or column_name.endswith(
                     "requisition_id"
                 ):
@@ -316,10 +307,8 @@ class ModelToDataframe:
             else:
                 raise
         for name in self.sys_field_names:
-            try:
+            with contextlib.suppress(ValueError):
                 columns_list.remove(name)
-            except ValueError:
-                pass
         if not self.decrypt:
             columns_list = [col for col in columns_list if col not in self.encrypted_columns]
         return columns_list
@@ -338,7 +327,6 @@ class ModelToDataframe:
     @property
     def list_columns(self) -> list[str]:
         """Return a list of column names with fk to a list model."""
-        from edc_list_data.model_mixins import ListModelMixin, ListUuidModelMixin
 
         if not self._list_columns:
             list_columns = []
@@ -348,14 +336,13 @@ class ModelToDataframe:
                     and fld_cls.related_model
                     and issubclass(fld_cls.related_model, (ListModelMixin, ListUuidModelMixin))
                 ):
-                    list_columns.append(fld_cls.attname)
+                    list_columns.append(fld_cls.attname)  # noqa: PERF401
             self._list_columns = list(set(list_columns))
         return self._list_columns
 
     @property
     def site_columns(self) -> list[str]:
         """Return a list of column names with fk to a site model."""
-        from django.contrib.sites.models import Site
 
         if not self._site_columns:
             site_columns = []
@@ -372,10 +359,6 @@ class ModelToDataframe:
     @property
     def other_columns(self) -> list[str]:
         """Return other column names with fk to a common models."""
-        from django.contrib.sites.models import Site
-
-        from edc_lab.models import Panel
-
         related_model = [Site, Panel]
         if not self._list_columns:
             list_columns = []

edc_model_to_dataframe/read_frame_edc.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 from django.apps import apps as django_apps
 from django.db.models import QuerySet
 
@@ -7,7 +9,7 @@ __all__ = ["read_frame_edc"]
 
 
 def read_frame_edc(
-    queryset: QuerySet | str = None,
+    queryset: QuerySet | str,
     drop_sys_columns: bool | None = None,
     drop_action_item_columns: bool | None = None,
     read_frame_verbose: bool | None = None,

edc_pdutils/dataframes/get_crf.py

@@ -6,7 +6,7 @@ from django.contrib.sites.models import Site
 from django.db import models
 from django_pandas.io import read_frame
 
-from edc_model_to_dataframe import read_frame_edc
+from edc_model_to_dataframe.read_frame_edc import read_frame_edc
 from edc_registration.models import RegisteredSubject
 
 from ..constants import SYSTEM_COLUMNS

edc_pdutils/df_exporters/csv_model_exporter.py

@@ -5,7 +5,7 @@ from typing import TYPE_CHECKING
 
 from django.core.management.color import color_style
 
-from edc_model_to_dataframe import ModelToDataframe
+from edc_model_to_dataframe.model_to_dataframe import ModelToDataframe
 
 from .csv_exporter import CsvExporter
 

edc_pdutils/management/commands/export_models.py

@@ -10,7 +10,7 @@ from django.core.exceptions import ObjectDoesNotExist
 from django.core.management import CommandError, color_style
 from django.core.management.base import BaseCommand
 
-from edc_model_to_dataframe import ModelToDataframe
+from edc_model_to_dataframe.model_to_dataframe import ModelToDataframe
 from edc_pdutils.df_exporters import Exporter
 from edc_pdutils.utils import get_model_names
 from edc_sites.site import sites

edc_pdutils/utils/missing_subject_identifiers.py

@@ -3,7 +3,7 @@ from warnings import warn
 import pandas as pd
 from django.apps import apps as django_apps
 
-from edc_model_to_dataframe import ModelToDataframe
+from edc_model_to_dataframe.model_to_dataframe import ModelToDataframe
 
 
 def missing_subject_identifiers(
@@ -42,7 +42,7 @@ def missing_subject_identifiers(
 
     if len(df_missing.index) > 0 and verbose:
         warn(
-            f'There are {len(df_missing["identifier"])} subject identifiers '
+            f"There are {len(df_missing['identifier'])} subject identifiers "
             f"missing from {model}."
         )
     return df_missing["identifier"]