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Snt25 518 #96

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efd6e98
first commit
EstebanMontandon Jun 10, 2026
7d8fae2
feat(map): try build pop table
EstebanMontandon Jun 10, 2026
34ac46f
feat(map): indicators computation per year
EstebanMontandon Jun 11, 2026
2519d25
fix(map): report (standard)
EstebanMontandon Jun 11, 2026
01687bc
fix(): reviews from copilot.
EstebanMontandon Jun 12, 2026
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ SNT Process/
.vscode/
venv/
uv.lock
__pycache__/

# Jupyter stuff -------------------------

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367 changes: 156 additions & 211 deletions pipelines/snt_map_extracts/reporting/snt_map_extracts_report.ipynb
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@@ -1,216 +1,161 @@
{
"cells": [
{
"cell_type": "markdown",
"id": "5777b72c-d87e-47c5-87b1-2698a6510b2f",
"metadata": {},
"source": [
"# **Cartes extraites du Malaria Atlas Project (MAP)**"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6397ab91-1ae4-4db7-b6c3-061c453a7b03",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# Set SNT Paths\n",
"SNT_ROOT_PATH <- \"~/workspace\"\n",
"CODE_PATH <- file.path(SNT_ROOT_PATH, \"code\")\n",
"CONFIG_PATH <- file.path(SNT_ROOT_PATH, \"configuration\")\n",
"PIPELINE_PATH <- file.path(SNT_ROOT_PATH, \"pipelines\", \"snt_map_extracts\")\n",
"\n",
"# load util functions\n",
"source(file.path(CODE_PATH, \"snt_utils.r\"))\n",
"source(file.path(PIPELINE_PATH, \"utils\", \"snt_map_extracts_report.r\"))\n",
"\n",
"# List required packages\n",
"required_packages <- c(\"dplyr\", \"tidyr\", \"terra\", \"ggplot2\", \"stringr\", \"lubridate\", \"viridis\", \"patchwork\", \"zoo\", \"purrr\", \"arrow\", \"sf\", \"reticulate\")\n",
"\n",
"# Execute function\n",
"install_and_load(required_packages)\n",
"\n",
"# Set environment to load openhexa.sdk from the right environment\n",
"Sys.setenv(RETICULATE_PYTHON = \"/opt/conda/bin/python\")\n",
"reticulate::py_config()$python\n",
"openhexa <- import(\"openhexa.sdk\")\n",
"\n",
"# Load SNT config\n",
"config_json <- tryCatch({ jsonlite::fromJSON(file.path(CONFIG_PATH, \"SNT_config.json\"))},\n",
" error = function(e) {\n",
" msg <- paste0(\"Error while loading configuration\", conditionMessage(e))\n",
" cat(msg)\n",
" stop(msg)\n",
" })\n",
"\n",
"# Required environment for the sf packages\n",
"Sys.setenv(PROJ_LIB = \"/opt/conda/share/proj\")\n",
"Sys.setenv(GDAL_DATA = \"/opt/conda/share/gdal\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "93e04996-13ba-4855-a1d1-46e70ba4640e",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# Configuration variables\n",
"DATASET_NAME <- config_json$SNT_DATASET_IDENTIFIERS$SNT_MAP_EXTRACT\n",
"COUNTRY_CODE <- config_json$SNT_CONFIG$COUNTRY_CODE\n",
"ADM_2 <- toupper(config_json$SNT_CONFIG$DHIS2_ADMINISTRATION_2)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a1ee21d1-c7d1-4893-ac56-91abb92926ea",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# printdim() loaded from utils/snt_map_extracts_report.r"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f7de799e-896c-4237-a9f6-9dafc0f30bde",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# import seasonality data\n",
"map_data <- load_map_report_input(\n",
" dataset_name = DATASET_NAME,\n",
" filename = paste0(COUNTRY_CODE, \"_map_data.parquet\"),\n",
" label = \"MAP extracted data\"\n",
")\n",
"\n",
"# import DHIS2 shapes data\n",
"DATASET_DHIS2 <- config_json$SNT_DATASET_IDENTIFIERS$DHIS2_DATASET_FORMATTED\n",
"shapes_data <- load_map_report_input(\n",
" dataset_name = DATASET_DHIS2,\n",
" filename = paste0(COUNTRY_CODE, \"_shapes.geojson\"),\n",
" label = \"DHIS2 shapes data\"\n",
")\n",
"\n",
"printdim(map_data)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "84031c7e-e9c6-4496-896f-7f7f3403d951",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"names(map_data)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "66b05b53-3f65-424a-af22-0686238a06c9",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"unique(map_data$METRIC_NAME)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9d0515ab-4dc2-4671-8c3c-236578a840d8",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# Merge geometry with map data\n",
"map_data_joined <- dplyr::left_join(shapes_data, map_data, by = c(\"ADM2_ID\" = \"ADM2_ID\"))\n",
"\n",
"# Get list of metrics\n",
"metrics <- unique(map_data$METRIC_NAME)\n",
"\n",
"# Create one map per metric\n",
"plots <- build_metric_plots(map_data_joined = map_data_joined, metrics = metrics)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0f1dc1df-211d-4174-83ae-e8ae974fa790",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# Set plot size for individual display\n",
"options(repr.plot.width = 10, repr.plot.height = 8)\n",
"\n",
"# Loop through plots and print one by one\n",
"for (p in plots) {\n",
" print(p)\n",
" Sys.sleep(1) # Optional: short pause between plots\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "50c843e4-9157-480d-acde-80887410d156",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": []
"cells": [
{
"cell_type": "markdown",
"id": "5777b72c-d87e-47c5-87b1-2698a6510b2f",
"metadata": {},
"source": [
"# **Cartes extraites du Malaria Atlas Project (MAP)**"
]
},
{
"cell_type": "markdown",
"id": "f0860675-9819-4a0a-b0ce-23f1b16d40c3",
"metadata": {},
"source": [
"## Setup"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "dfb0dee9-0da8-4afd-9f3a-7e8f0a830f85",
"metadata": {},
"outputs": [],
"source": [
"source(file.path(\"~/workspace/pipelines/snt_map_extracts/utils/snt_map_extracts_report.r\"))\n",
"setup_var <- get_setup_variables(packages= c(\"arrow\", \"dplyr\", \"tidyr\", \"stringr\", \"stringi\", \"jsonlite\", \"httr\", \"reticulate\", \"glue\"))\n",
"config_json <- load_snt_config(file.path(setup_var$CONFIG_PATH, \"SNT_config.json\"))\n",
"\n",
"# Save config variables\n",
"DATASET_MAP <- config_json$SNT_DATASET_IDENTIFIERS$SNT_MAP_EXTRACTS\n",
"DATASET_FORMATTED <- config_json$SNT_DATASET_IDENTIFIERS$DHIS2_DATASET_FORMATTED\n",
"COUNTRY_CODE <- config_json$SNT_CONFIG$COUNTRY_CODE"
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]
},
{
"cell_type": "markdown",
"id": "6b3456da-ddfd-4b9b-9c9b-506f583aab3e",
"metadata": {},
"source": [
"## Load Data"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f7de799e-896c-4237-a9f6-9dafc0f30bde",
"metadata": {
"vscode": {
"languageId": "r"
}
],
"metadata": {
"kernelspec": {
"display_name": "R",
"language": "R",
"name": "ir"
},
"language_info": {
"codemirror_mode": "r",
"file_extension": ".r",
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "4.4.3"
},
"outputs": [],
"source": [
"# Load parameters\n",
"map_parameters <- load_dataset_file(dataset_id = DATASET_MAP, filename = paste0(COUNTRY_CODE, \"_parameters.json\"))\n",
"cat(jsonlite::toJSON(map_parameters, pretty = TRUE, auto_unbox = TRUE), \"\\n\")\n",
"\n",
"# Load latest year file available\n",
"map_data <- load_dataset_file(dataset_id = DATASET_MAP, filename = glue(\"{COUNTRY_CODE}_map_data_{map_parameters$YEAR_END}.parquet\"))\n",
"\n",
"# import DHIS2 shapes data\n",
"shapes_data <- load_dataset_file(dataset_id = DATASET_FORMATTED, filename = paste0(COUNTRY_CODE, \"_shapes.geojson\"))\n",
"\n",
"printdim(map_data)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "66b05b53-3f65-424a-af22-0686238a06c9",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"print(glue(\"Year file selection: {map_parameters$YEAR_END}\"))\n",
"print(glue(\"Indicators: {unique(map_data$METRIC_NAME)}\"))"
]
},
{
"cell_type": "markdown",
"id": "0ea5587e-b7d3-47c1-a4b3-c69061d24bca",
"metadata": {},
"source": [
"## Create plots \n",
"\n",
"We select the latest year of the selected years based on the parameters run."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9d0515ab-4dc2-4671-8c3c-236578a840d8",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# Merge geometry with map data\n",
"map_data_joined <- dplyr::left_join(shapes_data, map_data, by = c(\"ADM2_ID\" = \"ADM2_ID\"))\n",
"\n",
"# Get list of metrics\n",
"metrics <- unique(map_data$METRIC_NAME)\n",
"\n",
"# Create one map per metric\n",
"plots <- build_metric_plots(map_data_joined = map_data_joined, metrics = metrics, year=map_parameters$YEAR_END)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0f1dc1df-211d-4174-83ae-e8ae974fa790",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"outputs": [],
"source": [
"# Set plot size for individual display\n",
"options(repr.plot.width = 10, repr.plot.height = 8)\n",
"\n",
"# Loop through plots and print one by one\n",
"for (p in plots) {\n",
" print(p)\n",
" Sys.sleep(1) # Optional: short pause between plots\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8eb9cc86-f3ed-45f2-84f3-9e395ef85106",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "R",
"language": "R",
"name": "ir"
},
"nbformat": 4,
"nbformat_minor": 5
"language_info": {
"codemirror_mode": "r",
"file_extension": ".r",
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "4.5.3"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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