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jonbrenasjonbrenas
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Merge pull request malariagen#1053 from adilraza99/GH435-cohort-geometries
Add cohort_geometries() to access cohort GeoJSON metadata
2 parents 5b3315e + a68d665 commit fe4f512

6 files changed

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‎malariagen_data/anoph/sample_metadata.py‎

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@@ -1,4 +1,5 @@
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import io
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import json
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from itertools import cycle
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from typing import (
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Any,
@@ -81,6 +82,7 @@ def __init__(
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# Initialize cache attributes.
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self._cache_sample_metadata: Dict = dict()
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self._cache_cohort_geometries: Dict = dict()
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8587
def _metadata_paths(
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self,
@@ -1527,6 +1529,59 @@ def cohorts(
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return df_cohorts
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@_check_types
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@doc(
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summary="""
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Read GeoJSON geometry data for a specific cohort set,
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providing boundary geometries for each cohort.
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""",
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parameters=dict(
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cohort_set="""
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A cohort set name. Accepted values are:
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"admin1_month", "admin1_quarter", "admin1_year",
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"admin2_month", "admin2_quarter", "admin2_year".
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""",
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),
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returns="""
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A dict containing the parsed GeoJSON FeatureCollection,
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with boundary geometries for each cohort in the set.
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""",
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)
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def cohort_geometries(
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self,
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cohort_set: base_params.cohorts,
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) -> dict:
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valid_cohort_sets = {
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"admin1_month",
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"admin1_quarter",
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"admin1_year",
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"admin2_month",
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"admin2_quarter",
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"admin2_year",
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}
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if cohort_set not in valid_cohort_sets:
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raise ValueError(
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f"{cohort_set!r} is not a valid cohort set. "
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f"Accepted values are: {sorted(valid_cohort_sets)}."
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)
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cohorts_analysis = self._cohorts_analysis
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# Cache to avoid repeated reads.
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cache_key = (cohorts_analysis, cohort_set)
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try:
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geojson_data = self._cache_cohort_geometries[cache_key]
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except KeyError:
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major_version_path = self._major_version_path
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path = f"{major_version_path[:2]}_cohorts/cohorts_{cohorts_analysis}/cohorts_{cohort_set}.geojson"
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with self.open_file(path) as f:
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geojson_data = json.load(f)
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self._cache_cohort_geometries[cache_key] = geojson_data
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return geojson_data
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15301585
@_check_types
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@doc(
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summary="""

‎notebooks/cohort_geometries.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Cohort Geometries\n",
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"\n",
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"Demonstrates the `cohort_geometries()` method for accessing GeoJSON boundary data."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import malariagen_data"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Set up the Ag3 data resource"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"ag3 = malariagen_data.Ag3(\n",
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" \"simplecache::gs://vo_agam_release_master_us_central1\",\n",
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" simplecache=dict(cache_storage=\"../gcs_cache\"),\n",
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")\n",
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"ag3"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Access cohort geometries"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"geojson = ag3.cohort_geometries(cohort_set=\"admin1_year\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Inspect the returned data"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"type(geojson)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"geojson.keys()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"len(geojson[\"features\"])"
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]
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},
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{
92+
"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
97+
"for f in geojson[\"features\"][:3]:\n",
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" print(f[\"properties\"])"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"name": "python",
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"version": "3.10.0"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎tests/anoph/conftest.py‎

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@@ -1426,6 +1426,29 @@ def write_metadata(
14261426
for line in src.readlines()[:5]:
14271427
print(line, file=dst)
14281428

1429+
# Copy cohort GeoJSON fixtures.
1430+
geojson_files = [
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"cohorts_admin1_month.geojson",
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"cohorts_admin1_year.geojson",
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]
1434+
for geojson_file in geojson_files:
1435+
src_path = (
1436+
self.fixture_dir
1437+
/ "vo_agam_release_master_us_central1"
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/ "v3_cohorts"
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/ "cohorts_20230516"
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/ geojson_file
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)
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if src_path.exists():
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dst_path = (
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self.bucket_path
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/ "v3_cohorts"
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/ "cohorts_20230516"
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/ geojson_file
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)
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dst_path.parent.mkdir(parents=True, exist_ok=True)
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shutil.copy2(src_path, dst_path)
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14291452
# Create data catalog by sampling from some real metadata files.
14301453
src_path = (
14311454
self.fixture_dir

‎tests/anoph/fixture/vo_agam_release_master_us_central1/v3_cohorts/cohorts_20230516/cohorts_admin1_month.geojson‎

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{
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"type": "FeatureCollection",
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"features": [
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{
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"type": "Feature",
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"properties": {
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"cohort_id": "BF-01_arab_2008_04",
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"admin1_name": "Boucle du Mouhoun",
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"admin1_iso": "BF-01"
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},
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"geometry": {
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"type": "Polygon",
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"coordinates": [[[-4.5, 12.0], [-3.5, 12.0], [-3.5, 13.0], [-4.5, 13.0], [-4.5, 12.0]]]
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}
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},
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{
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"type": "Feature",
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"properties": {
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"cohort_id": "BF-02_colu_2011_07",
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"admin1_name": "Cascades",
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"admin1_iso": "BF-02"
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},
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"geometry": {
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"type": "Polygon",
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"coordinates": [[[-5.0, 10.0], [-4.0, 10.0], [-4.0, 11.0], [-5.0, 11.0], [-5.0, 10.0]]]
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}
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}
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]
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}

‎tests/anoph/fixture/vo_agam_release_master_us_central1/v3_cohorts/cohorts_20230516/cohorts_admin1_year.geojson‎

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{
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"type": "FeatureCollection",
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"features": [
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{
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"type": "Feature",
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"properties": {
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"cohort_id": "AO-LUA_colu_2009",
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"admin1_name": "Luanda",
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"admin1_iso": "AO-LUA"
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},
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"geometry": {
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"type": "Polygon",
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"coordinates": [[[13.0, -10.0], [14.0, -10.0], [14.0, -9.0], [13.0, -9.0], [13.0, -10.0]]]
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}
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},
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{
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"type": "Feature",
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"properties": {
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"cohort_id": "BF-01_arab_2008",
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"admin1_name": "Boucle du Mouhoun",
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"admin1_iso": "BF-01"
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},
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"geometry": {
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"type": "Polygon",
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"coordinates": [[[-4.5, 12.0], [-3.5, 12.0], [-3.5, 13.0], [-4.5, 13.0], [-4.5, 12.0]]]
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}
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}
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]
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}

‎tests/anoph/test_sample_metadata.py‎

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@@ -1465,3 +1465,48 @@ def test_cohort_data(fixture, api):
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df_cohorts = api.cohorts(cohort_name)
14661466
# Check output.
14671467
validate_cohort_data(df_cohorts, cohort_data_expected_columns())
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1469+
1470+
# ------------------------------------------------------------------
1471+
# Tests for cohort_geometries()
1472+
# ------------------------------------------------------------------
1473+
1474+
1475+
@parametrize_with_cases("fixture,api", cases=case_ag3_sim)
1476+
def test_cohort_geometries(fixture, api):
1477+
"""Test that GeoJSON geometry can be loaded for a valid cohort set."""
1478+
geojson = api.cohort_geometries("admin1_month")
1479+
assert isinstance(geojson, dict)
1480+
assert geojson["type"] == "FeatureCollection"
1481+
assert "features" in geojson
1482+
assert len(geojson["features"]) > 0
1483+
for feature in geojson["features"]:
1484+
assert feature["type"] == "Feature"
1485+
assert "geometry" in feature
1486+
assert "properties" in feature
1487+
assert "coordinates" in feature["geometry"]
1488+
1489+
1490+
@parametrize_with_cases("fixture,api", cases=case_ag3_sim)
1491+
def test_cohort_geometries_admin1_year(fixture, api):
1492+
"""Test that GeoJSON geometry can be loaded for admin1_year."""
1493+
geojson = api.cohort_geometries("admin1_year")
1494+
assert isinstance(geojson, dict)
1495+
assert geojson["type"] == "FeatureCollection"
1496+
assert len(geojson["features"]) > 0
1497+
1498+
1499+
@parametrize_with_cases("fixture,api", cases=case_ag3_sim)
1500+
def test_cohort_geometries_invalid_cohort_set(fixture, api):
1501+
"""Test that an invalid cohort_set raises ValueError."""
1502+
with suppress_type_checks():
1503+
with pytest.raises(ValueError, match="not a valid cohort set"):
1504+
api.cohort_geometries("invalid_set")
1505+
1506+
1507+
@parametrize_with_cases("fixture,api", cases=case_ag3_sim)
1508+
def test_cohort_geometries_cached(fixture, api):
1509+
"""Test that the second call returns the same cached object."""
1510+
g1 = api.cohort_geometries("admin1_month")
1511+
g2 = api.cohort_geometries("admin1_month")
1512+
assert g1 is g2

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