SNT25-488 (snt_dhis2_extract_report)

[sPuntinG]

SNT25-488 --- Reporting nb + r utils of reporting of "A.1 DHIS2 Extract"

https://bluesquare.atlassian.net/browse/SNT25-488

Done

• Cleaned code by replacing set up and config code with equivalent functions from ./code/snt_utils.r
• changed the display of first table of "Liste des éléments de donnée extraits" (disaggregatedd indicators) to be also not kable() style (it was confusing to have 2 rendering styles, and kable outputs are truncated when too long)
• changed color of missing values from "tomatoe" to "grey" in plots "Complétude de l'extraction des données de routine au niveau des formations sanitaires"
• In "6. Disponibilité des données par formation sanitaire (sur la période analysée)" fixed some phrasing that was either wrong ("une valeur non manquante (c’est-à-dire, une donnée rapportée, qu’elle soit nulle ou positive)") or confusiong ("fenetre" for denominator, and phrasing of subtitle).
• Made y axis start from 0 in all plots to be less dramatic/misleading ...

Yet to be addressed (not great but not breaking):

• At point ### 6.: 🤌🏼 # GP (2026-08-06): why do we get "white" (or blank) tiles? Missing data should get a 0% ...
• Double import of routine_data because at step ### 5. it is transformed and overwritten, so if used as is it breaks at point ### 7. (hence need to keep the second import from dataset). See comment: ⚠️ # GP: need to keep this import and transformation even if repeated from upstream) ...

Tested in:

• 🇨🇩 COD ("SNT Testing")
• 🇧🇮 BDI ("BDI SNT Process"). Note: current pipeline version is outdated, so I added the utils file manually so I could test the dev version of the reporting ipynb via VS Code (R reporting utils would be pulled if the pipeline was updated and re-run with "Pull scripts"). This way I don't mess up the ws in case they need to use that specific run.

☑️ Also checked: it renders in Orchestrator WebApp html embedded preview

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⛙ Important: always merge branch with Rebase so changes are replayed on top (avoid re-surfacing of older code)

[irautu-bluesquare]

Nice work, mentioned some minor changes, most of them can be added for a future rework if you don't have time now

Nothing breaking. Keep comments as suggestions for later. Reviewer on leave and I need to merge.