From 8a4c9537913007770244cb974a0a01f63a2852df Mon Sep 17 00:00:00 2001
From: Fiona Spooner <fiona@ourworldindata.org>
Date: Tue, 20 Aug 2024 20:09:47 +0100
Subject: [PATCH] =?UTF-8?q?=E2=9C=A8=20Adding=20DRC=20annotation=20(#3159)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* adding DRC annotation

* add annotation

* update

* set index

* add annotation

* attempting garden

* update origins
---
 .../data/garden/who/latest/monkeypox/__init__.py   | 14 +++++++++++++-
 .../garden/who/latest/monkeypox/monkeypox.meta.yml | 10 ++++++++++
 etl/steps/data/grapher/who/latest/monkeypox.py     |  1 -
 3 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/etl/steps/data/garden/who/latest/monkeypox/__init__.py b/etl/steps/data/garden/who/latest/monkeypox/__init__.py
index 436debea576..966f0b6c971 100644
--- a/etl/steps/data/garden/who/latest/monkeypox/__init__.py
+++ b/etl/steps/data/garden/who/latest/monkeypox/__init__.py
@@ -32,7 +32,7 @@ def run(dest_dir: str) -> None:
     # Read table from meadow dataset.
     tb = ds_meadow["monkeypox"].reset_index()
     tb_suspected = ds_suspected["africa_cdc"].reset_index()
-
+    origins = tb["total_conf_cases"].metadata.origins
     #
     # Process data.
     #
@@ -54,6 +54,18 @@ def run(dest_dir: str) -> None:
     )
 
     tb_both = pr.merge(tb, tb_suspected, on=["country", "date"], how="outer")
+
+    # For variables on deaths we should show that data reported by the WHO show _only_ confirmed cases, in an annotation
+    country_mask = tb_both["country"] == "Democratic Republic of Congo"
+    tb_both["annotation"] = ""
+    for col in tb_both.columns:
+        if "deaths" in col:
+            # Update the annotation column for matching rows
+            tb_both.loc[country_mask, "annotation"] = (
+                tb_both.loc[country_mask, "annotation"]
+                + "Democratic Republic of Congo: Includes only confirmed deaths as reported by WHO"
+            )
+    tb_both["annotation"].metadata.origins = origins
     tb_both = tb_both.format(["country", "date"])
 
     #
diff --git a/etl/steps/data/garden/who/latest/monkeypox/monkeypox.meta.yml b/etl/steps/data/garden/who/latest/monkeypox/monkeypox.meta.yml
index 128b2f31433..47a9ab935ea 100644
--- a/etl/steps/data/garden/who/latest/monkeypox/monkeypox.meta.yml
+++ b/etl/steps/data/garden/who/latest/monkeypox/monkeypox.meta.yml
@@ -5,6 +5,7 @@ definitions:
       topic_tags:
         - Mpox (monkeypox)
 
+
 dataset:
   update_period_days: 365
 
@@ -21,6 +22,7 @@ tables:
         unit: deaths
         display:
           numDecimalPlaces: 0
+          entityAnnotationsMap: "Democratic Republic of Congo: Includes only confirmed deaths as reported by WHO"
       new_cases:
         title: New confirmed cases
         unit: cases
@@ -31,6 +33,7 @@ tables:
         unit: deaths
         display:
           numDecimalPlaces: 0
+          entityAnnotationsMap: "Democratic Republic of Congo: Includes only confirmed deaths as reported by WHO"
       new_cases_smoothed:
         title: New confirmed cases (7-day smoothed)
         unit: cases
@@ -41,6 +44,7 @@ tables:
         unit: deaths
         display:
           numDecimalPlaces: 2
+          entityAnnotationsMap: "Democratic Republic of Congo: Includes only confirmed deaths as reported by WHO"
       new_cases_per_million:
         title: New confirmed cases per million
         unit: cases per million
@@ -61,16 +65,22 @@ tables:
         unit: deaths per million
         display:
           numDecimalPlaces: 3
+          entityAnnotationsMap: "Democratic Republic of Congo: Includes only confirmed deaths as reported by WHO"
       total_deaths_per_million:
         title: Total confirmed deaths per million
         unit: deaths per million
         display:
           numDecimalPlaces: 3
+          entityAnnotationsMap: "Democratic Republic of Congo: Includes only confirmed deaths as reported by WHO"
       new_deaths_smoothed_per_million:
         title: New confirmed deaths per million (7-day smoothed)
         unit: deaths per million
         display:
           numDecimalPlaces: 3
+          entityAnnotationsMap: "Democratic Republic of Congo: Includes only confirmed deaths as reported by WHO"
       iso_code:
         title: ISO code
         unit: ''
+      annotation:
+        title: Annotation
+        unit: ''
diff --git a/etl/steps/data/grapher/who/latest/monkeypox.py b/etl/steps/data/grapher/who/latest/monkeypox.py
index 697d5f1da22..9a157d6bb54 100644
--- a/etl/steps/data/grapher/who/latest/monkeypox.py
+++ b/etl/steps/data/grapher/who/latest/monkeypox.py
@@ -16,7 +16,6 @@ def run(dest_dir: str) -> None:
     # Read table from garden dataset.
     tb = ds_garden["monkeypox"]
 
-    #
     # Save outputs.
     #
     # Create a new grapher dataset with the same metadata as the garden dataset.