edc-qareports 0.1.20

Classes for QA Reports in clinicedc/edc projects

edc-qareports

This module helps you represent SQL VIEWS as QA Reports using Django Admin.

In clinicedc/edc projects, QA reports are in the <my_app>_reports module.

Installation

Add to settings.INSTALLED_APPS:

INSTALLED_APPS = [
    ...
    "edc_qareports.apps.AppConfig",
    ...
    ]

Add to project URLS:

# urls.py
urlpatterns = [
    ...
    *paths_for_urlpatterns("edc_qareports"),
    ...
    ]

Custom QA / data management reports using SQL VIEWS

Although not absolutely necessary, it is convenient to base a QA report on an SQL VIEW. As data issues are resolved, the SQL VIEW reflects the current data.

A QA report based on an SQL VIEW can be represented by a model class. By registering the model class in Admin, all the functionality of the ModelAdmin class is available to show the report.

First, within your EDC project, create a <myapp>_reports app. For example Meta Reports.

meta_edc
meta_edc/meta_reports
meta_edc/meta_reports/admin
meta_edc/meta_reports/admin/dbviews
meta_edc/meta_reports/admin/dbviews/my_view_in_sql_admin.py
meta_edc/meta_reports/migrations
meta_edc/meta_reports/migrations/0001_myviewinsql.py
meta_edc/meta_reports/models
meta_edc/meta_reports/models/dbviews
meta_edc/meta_reports/models/dbviews/mymodel/unmanaged_model.py
meta_edc/meta_reports/models/dbviews/mymodel/view_definition.py
meta_edc/meta_reports/admin_site.py
meta_edc/meta_reports/apps.py
meta_edc/ ...

the apps.py might look like this:

from django.apps import AppConfig as DjangoAppConfig

class AppConfig(DjangoAppConfig):
    name = "meta_reports"
    verbose_name = "META Reports"
    include_in_administration_section = True

QA Report as an SQL VIEW

Now that you have created the basic structure for the Reports App, create an SQL VIEW. Some rules apply:

• To show the model class in Admin, the SQL VIEW needs at least an ID column.

• To use the EDC ModelAdmin classes, include id, subject_identifier, site_id, created and report_model.

• Columns id, created and report_model are generated columns from the SQL VIEW, not values coming from the underlying SQL statement / data tables.

• Column report_model is in label_lower format.

• Suffix the view name with _view.

To manage SQL view code, we use django_dbviews. This module helps by using migrations to manage changes to the SQL view code.

The view_defintion.py might look like this:

from edc_qareports.sql_generator import SqlViewGenerator

def get_view_definition() -> dict:
    subquery = """
        select subject_identifier, site_id, appt_datetime, `first_value`,
        `second_value`, `third_value`,
        datediff(`third_date`, `first_date`) as `interval_days`,
        datediff(now(), `first_date`) as `from_now_days`
        from (
            select subject_identifier, site_id, appt_datetime,
            FIRST_VALUE(visit_code) OVER w as `first_value`,
            NTH_VALUE(visit_code, 2) OVER w as `second_value`,
            NTH_VALUE(visit_code, 3) OVER w as `third_value`,
            FIRST_VALUE(appt_datetime) OVER w as `first_date`,
            NTH_VALUE(appt_datetime, 3) OVER w as `third_date`
            from edc_appointment_appointment where visit_code_sequence=0 and appt_status="New"
            and appt_datetime <= now()
            WINDOW w as (PARTITION BY subject_identifier order by appt_datetime ROWS UNBOUNDED PRECEDING)
        ) as B
        where `second_value` is not null and `third_value` is not null
        """  # noqa
    sql_view = SqlViewGenerator(
        report_model="meta_reports.unattendedthreeinrow",
        ordering=["subject_identifier", "site_id"],
    )
    return {
        "django.db.backends.mysql": sql_view.as_mysql(subquery),
        "django.db.backends.postgresql": sql_view.as_postgres(subquery),
        "django.db.backends.sqlite3": sql_view.as_sqlite(subquery),
    }

Using a model class to represent your QA Report

An SQL VIEW is not a table so configure an unmanaged model class by setting managed=False. makemigrations creates migrations for unmanaged models but never calls CreateModel.

The unmanaged model class would be something like this:

class MyViewInSql(QaReportModelMixin, models.Model):

    col1 = models.CharField(max_length=25)

    col2 = models.IntegerField()

    col3 = models.DateTimeField()

    class Meta:
        managed = False
        db_table = "my_view_in_sql_view"
        verbose_name = "blah blah"
        verbose_name_plural = "blah blah"

You can store the SQL statement anywhere but we put it in the same folder as the model class using the same file name as the model class but with file extension .sql

Using a migration to read the SQL statement

Create an empty migration in the reports app and read the SQL file in the migration

...

operations = [
    migrations.RunSQL(
        read_unmanaged_model_sql("my_view_in_sql.sql", app_name="meta_reports")
    ),
]

IMPORTANT: If you change the SQL VIEW, update the .sql file and create a new migration that drops and re-creates the SQL VIEW.

...

operations = [
    migrations.RunSQL("drop view my_view_in_sql_view"),
    migrations.RunSQL(
        read_unmanaged_model_sql("my_view_in_sql.sql", app_name="meta_reports")
    ),
]

Linking QaReportNote with your QA Report

You can link your QA Report in Admin to model QaReportNote. The QaReportNote model class is used to track the status of the report item and provide a space for any notes.

To use QaReportNote with your QA report, declare the QA Report admin class with QaReportWithNoteModelAdminMixin.

from django.contrib import admin
from edc_model_admin.dashboard import ModelAdminDashboardMixin
from edc_model_admin.mixins import TemplatesModelAdminMixin
from edc_qareports.admin import QaReportWithNoteModelAdminMixin
from edc_sites.admin import SiteModelAdminMixin
from edc_visit_schedule.admin import ScheduleStatusListFilter

from ...admin_site import meta_reports_admin
from ...models import MyViewInSql


@admin.register(MyViewInSql, site=meta_reports_admin)
class MyViewInSqlAdmin(
    QaReportWithNoteModelAdminMixin,
    SiteModelAdminMixin,
    ModelAdminDashboardMixin,
    TemplatesModelAdminMixin,
    admin.ModelAdmin,
):
    ordering = ["site", "subject_identifier"]

    list_display = [
        "dashboard",
        "subject",
        "col1",
        "col2",
        "col3",
        "created",
    ]

    list_filter = [ScheduleStatusListFilter, "col1", "col3"]

    search_fields = ["id", "subject_identifier"]

    @admin.display(description="Subject", ordering="subject_identifier")
    def subject(self, obj):
        return obj.subject_identifier

Granting access to your QA Report

Add the QA report codenames to your local app, create a group and add the group to the QA_REPORTS_ROLE.

In this example the app is called meta_reports and the group is META_REPORTS.

(Note: If your app has an auth module (e.g. meta_auth) put these lines there.)

# meta_reports/auth_objects.py

reports_codenames = [c for c in get_app_codenames("meta_reports")]

# meta_reports/auths.py

site_auths.add_group(*reports_codenames, name=META_REPORTS)
# add the group to the QA_REPORTS role
site_auths.update_role(META_REPORTS, name=QA_REPORTS_ROLE)