Merge branch 'release/0.1.14' into main

edc_qareports/model_mixins/__init__.py

@@ -1,3 +1,4 @@
 from .note_model_mixin import NoteModelMixin
+from .on_study_missing_values_model_mixin import OnStudyMissingValuesModelMixin
 from .qa_report_model_mixin import QaReportModelMixin
 from .qa_reports_permissions import qa_reports_permissions

edc_qareports/model_mixins/on_study_missing_values_model_mixin.py

@@ -0,0 +1,24 @@
+from django.db import models
+
+
+class OnStudyMissingValuesModelMixin(models.Model):
+    original_id = models.UUIDField(null=True)
+
+    label_lower = models.CharField(max_length=150, null=True)
+
+    subject_visit_id = models.UUIDField(null=True)
+
+    report_datetime = models.DateTimeField(null=True)
+
+    label = models.CharField(max_length=50, null=True)
+
+    visit_code = models.CharField(max_length=25, null=True)
+
+    visit_code_sequence = models.IntegerField(null=True)
+
+    schedule_name = models.CharField(max_length=25, null=True)
+
+    modified = models.DateTimeField(null=True)
+
+    class Meta:
+        abstract = True

edc_qareports/modeladmin_mixins/__init__.py

@@ -1,3 +1,6 @@
 from .list_filters import NoteStatusListFilter
 from .note_modeladmin_mixin import NoteModelAdminMixin
+from .on_study_missing_values_modeladmin_mixin import (
+    OnStudyMissingValuesModelAdminMixin,
+)
 from .qa_report_modeladmin_mixin import QaReportModelAdminMixin

edc_qareports/modeladmin_mixins/on_study_missing_values_modeladmin_mixin.py

@@ -0,0 +1,73 @@
+from django.apps import apps as django_apps
+from django.contrib import admin
+from django.template.loader import render_to_string
+from django.urls import reverse
+from django.utils.translation import gettext as _
+from edc_model_admin.dashboard import ModelAdminDashboardMixin
+from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_sites.admin import SiteModelAdminMixin
+from edc_visit_schedule.admin import ScheduleStatusListFilter
+
+from .qa_report_modeladmin_mixin import QaReportModelAdminMixin
+
+
+class OnStudyMissingValuesModelAdminMixin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+):
+    include_note_column: bool = True
+    project_reports_admin: str = "meta_reports_admin"
+    project_subject_admin: str = "meta_subject_admin"
+
+    ordering = ["site", "subject_identifier"]
+
+    list_display = [
+        "dashboard",
+        "subject_identifier",
+        "site",
+        "label",
+        "crf",
+        "visit",
+        "report_date",
+        "created",
+    ]
+
+    list_filter = [
+        ScheduleStatusListFilter,
+        "label",
+        "visit_code",
+        "report_datetime",
+    ]
+
+    search_fields = ["subject_identifier", "label"]
+
+    def dashboard(self, obj=None, label=None) -> str:
+        url = self.get_subject_dashboard_url(obj=obj)
+        if not url:
+            url = reverse(
+                f"{self.project_subject_admin}:{obj.label_lower.replace('.', '_')}_change",
+                args=(obj.original_id,),
+            )
+            url = (
+                f"{url}?next={self.project_reports_admin}:"
+                f"{self.model._meta.label_lower.replace('.', '_')}_changelist"
+            )
+        context = dict(title=_("Go to CRF"), url=url, label=label)
+        return render_to_string("dashboard_button.html", context=context)
+
+    @admin.display(description="CRF", ordering="label_lower")
+    def crf(self, obj=None) -> str:
+        model_cls = django_apps.get_model(obj.label_lower)
+        return model_cls._meta.verbose_name
+
+    @admin.display(description="Visit", ordering="visit_code")
+    def visit(self, obj=None) -> str:
+        return f"{obj.visit_code}.{obj.visit_code_sequence}"
+
+    @admin.display(description="Report date", ordering="report_datetime")
+    def report_date(self, obj) -> str | None:
+        if obj.report_datetime:
+            return obj.report_datetime.date()
+        return None

edc_qareports/sql_generator/__init__.py

@@ -0,0 +1,3 @@
+from .generate_subquery_for_missing_values import generate_subquery_for_missing_values
+from .select_from import SelectFrom
+from .sql_view_generator import SqlViewGenerator

edc_qareports/sql_generator/generate_subquery_for_missing_values.py

@@ -0,0 +1,29 @@
+from .select_from import SelectFrom
+
+
+def generate_subquery_for_missing_values(
+    cases: list[dict[str:str, str:str, str:str]],
+    as_list: bool | None = False,
+) -> str | list:
+    """Returns an SQL select statement as a union of the select
+    statements of each case.
+
+    args:
+     cases = [{
+         "label_lower": "my_app.hivhistory",
+         "dbtable": "my_app_hivhistory",
+         "field": "hiv_init_date",
+         "label": "missing HIV initiation date",
+         "list_tables": [(list_field, list_dbtable, alias), ...],
+         }, ...]
+
+         Note: `list_field` is the CRF id field, for example:
+            left join <list_dbtable> as <alias> on crf.<list_field>=<alias>.id
+    """
+    select_from_list = []
+    for case in cases:
+        select_from = SelectFrom(**case)
+        select_from_list.append(select_from.sql)
+    if as_list:
+        return select_from_list
+    return " UNION ".join(select_from_list)

edc_qareports/sql_generator/select_from.py

@@ -0,0 +1,39 @@
+from dataclasses import dataclass, field
+
+
+@dataclass(kw_only=True)
+class SelectFrom:
+    label: str = None
+    label_lower: str = None
+    dbtable: str = None
+    fld_name: str | None = None
+    where: str | None = None
+    list_tables: list[tuple[str, str, str]] | None = field(default_factory=list)
+    template: str = field(
+        init=False,
+        default="select v.subject_identifier, crf.id as original_id, crf.subject_visit_id, crf.report_datetime, crf.site_id, v.visit_code, v.visit_code_sequence, v.schedule_name, crf.modified, '{label_lower}' as label_lower, '{label}' as label, count(*) as records from {dbtable} as crf left join meta_subject_subjectvisit as v on v.id=crf.subject_visit_id {left_joins} where {where} group by v.subject_identifier, crf.subject_visit_id, crf.report_datetime, crf.site_id, v.visit_code, v.visit_code_sequence, v.schedule_name, crf.modified",  # noqa
+    )
+    sql: str | None = field(init=False, default=None)
+
+    def __post_init__(self):
+        if self.where is None:
+            self.where = f"crf.{self.fld_name} is null"
+        self.sql = self.template.format(
+            label=self.label,
+            label_lower=self.label_lower,
+            dbtable=self.dbtable,
+            where=self.where,
+            left_joins=self.left_joins,
+        )
+        self.sql = self.sql.replace(";", "")
+
+    @property
+    def left_joins(self) -> str:
+        """Add list tbls to access list cols by 'name' instead of 'id'"""
+        left_join = []
+        for opts in self.list_tables or []:
+            list_field, list_dbtable, alias = opts
+            left_join.append(
+                f"left join {list_dbtable} as {alias} on crf.{list_field}={alias}.id"
+            )
+        return " ".join(left_join)

edc_qareports/sql_generator/sql_view_generator.py

@@ -0,0 +1,73 @@
+from dataclasses import dataclass, field
+
+import sqlglot
+
+
+@dataclass(kw_only=True)
+class SqlViewGenerator:
+    """A class to generate SQL view statements given a select
+    statement.
+
+    Generated SQL is compatible with mysql, pgsql and sqlite3.
+
+    The given `select_statment` is not validated.
+
+    For use with view definitions.
+    """
+
+    report_model: str = None
+    ordering: list[str] | None = field(default_factory=list)
+    order_by: str | None = field(init=False, default=None)
+    with_stmt: str | None = field(default="")
+    footer: str = field(init=False, default=None)
+    template: str | None = field(
+        default="{with_stmt} {select_stmt} from ({subquery}) as A ORDER BY {order_by};"
+    )
+
+    def __post_init__(self):
+        ordering = [f"{fld[1:]} desc" if fld.startswith("~") else fld for fld in self.ordering]
+        self.order_by = ", ".join(ordering) or "subject_identifier"
+        self.footer = f") as A ORDER BY {self.order_by}"
+
+    @staticmethod
+    def transpile(sql: str, read: str | None = None, write: str = None) -> str:
+        read = read or "mysql"
+        sql = sql.replace(";", "")
+        return sqlglot.transpile(sql, read=read, write=write)[0]
+
+    def as_mysql(self, subquery: str, read: str | None = None) -> str:
+        select_stmt = f"select *, uuid() as id, now() as `created`, '{self.report_model}' as `report_model`"  # noqa
+        subquery = self.transpile(subquery, read=read, write="mysql")
+        return self.template.format(
+            with_stmt=self.with_stmt,
+            select_stmt=select_stmt,
+            subquery=subquery,
+            order_by=self.order_by,
+        )
+
+    def as_postgres(self, subquery: str, read: str | None = None) -> str:
+        select_stmt = f"select *, get_random_uuid() as id, now() as created, '{self.report_model}' as report_model"  # noqa
+        subquery = self.transpile(subquery, read=read, write="postgres")
+        return self.template.format(
+            with_stmt=self.with_stmt,
+            select_stmt=select_stmt,
+            subquery=subquery,
+            order_by=self.order_by,
+        )
+
+    def as_sqlite(self, subquery: str, read: str | None = None) -> str:
+        """For UUID support in sqlite, install sqlite/uuid.
+        See https://github.com/nalgeon/sqlpkg-cli?tab=readme-ov-file
+        and https://sqlpkg.org/?q=uuid
+
+            $ curl -sS https://webi.sh/sqlpkg | sh
+            $ sqlpkg install sqlite/uuid
+        """
+        select_stmt = f"select *, uuid() as id, datetime() as created, '{self.report_model}' as report_model"  # noqa
+        subquery = self.transpile(subquery, read=read, write="sqlite")
+        return self.template.format(
+            with_stmt=self.with_stmt,
+            select_stmt=select_stmt,
+            subquery=subquery,
+            order_by=self.order_by,
+        )

setup.cfg

@@ -13,6 +13,7 @@ classifiers=
     Environment :: Web Environment
     Framework :: Django
     Framework :: Django :: 4.2
+    Framework :: Django :: 5.1
     Intended Audience :: Developers
     Intended Audience :: Science/Research
     Operating System :: OS Independent
@@ -25,6 +26,8 @@ python_requires = >=3.12
 zip_safe = False
 include_package_data = True
 packages = find:
+install_requires =
+    sqlglot[rs]
 
 [options.packages.find]
 exclude =