From c15774e42229d712d114ce39daf6eb7f969876a5 Mon Sep 17 00:00:00 2001 From: Victoria McDonald <49625194+torimcd@users.noreply.github.com> Date: Wed, 30 Oct 2024 17:27:06 -0700 Subject: [PATCH] Feature/issue 258 - Granules with large numbers of features cannot be loadedd (#259) * change assemble attrs function to avoid for loop * change how attributes are concatenated during shp unpack to avoid slow looping * remove unused import * Update API test data with less precise data coordinates * remove logging every item in batch writer * lint --------- Co-authored-by: Nikki <17799906+nikki-t@users.noreply.github.com> --- CHANGELOG.md | 1 + hydrocron/db/io/swot_shp.py | 21 +- hydrocron/db/load_data.py | 4 + hydrocron/db/schema.py | 5 - tests/test_data/api_query_results_csv.csv | 2 +- .../test_data/api_query_results_geojson.json | 1124 ++++++++--------- .../api_query_results_geojson_compact.json | 1124 ++++++++--------- .../api_query_results_geojson_lakes.json | 4 +- 8 files changed, 1141 insertions(+), 1144 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 566ef3c..12e8a1b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Deprecated ### Removed ### Fixed + - Issue 258 - Granules with very large feature counts cannot be added to hydrocron - Issue 235 - Track ingest table can be populated with granules that aren't loaded into Hydrocron - Issue 248 - Track ingest operations need to query UAT for granule files if track ingest is running in SIT or UAT ### Security diff --git a/hydrocron/db/io/swot_shp.py b/hydrocron/db/io/swot_shp.py index 6c5466f..8b0c5ec 100644 --- a/hydrocron/db/io/swot_shp.py +++ b/hydrocron/db/io/swot_shp.py @@ -2,7 +2,6 @@ Unpacks SWOT Shapefiles """ import os.path -import json import tempfile from datetime import datetime, timezone from importlib import resources @@ -109,7 +108,7 @@ def handle_null_geometries(geodf): geodf_no_nulls : geopandas.GeoDataFrame the geodataframe with null geometries handled """ - + logging.info('Starting handle null geometries') geodf['geometry'].fillna( value=Polygon(constants.SWOT_PRIOR_LAKE_FILL_GEOMETRY_COORDS), inplace=True) @@ -131,6 +130,8 @@ def convert_polygon_to_centerpoint(geodf_polygon): geodf_centerpoint : geopandas.GeoDataFrame the geodataframe with point feature types and calculated centerpoint geometries """ + logging.info('Starting convert polygon to centerpoint') + geodf_centerpoint = geodf_polygon geodf_centerpoint['geometry'] = geodf_polygon['geometry'].centroid @@ -152,6 +153,7 @@ def parse_metadata_from_shpxml(xml_elem): metadata_attrs : dict a dictionary of metadata attributes to add to record """ + logging.info('Starting parse metadata from shpfile') # get SWORD version for globs in xml_elem.findall('global_attributes'): prior_db_files = globs.find('xref_prior_river_db_files').text @@ -191,18 +193,13 @@ def assemble_attributes(geodf, attributes): attributes : dict A dictionary of attributes to concatenate """ + logging.info('Starting assemble attributes') items = [] - # rework to use dataframe instead of file as string - for _index, row in geodf.iterrows(): - - shp_attrs = json.loads( - row.to_json(default_handler=str)) - item_attrs = shp_attrs | attributes - - item_attrs = {key: str(item_attrs[key]) for key in item_attrs.keys()} - items.append(item_attrs) + geodf = geodf.astype(str) + geodf = geodf.assign(**attributes) + items = geodf.to_dict('records') return items @@ -222,7 +219,7 @@ def parse_from_filename(filename): filename_attrs : dict A dictionary of attributes from the filename """ - + logging.info('Starting parse attributes from filename') filename_components = filename.split("_") collection = "" diff --git a/hydrocron/db/load_data.py b/hydrocron/db/load_data.py index d031bca..4ce20dd 100755 --- a/hydrocron/db/load_data.py +++ b/hydrocron/db/load_data.py @@ -365,8 +365,12 @@ def load_data(dynamo_resource, table_name, items): logging.info("Item %s: %s", feature_id, items[i][feature_id]) hydrocron_table.batch_fill_table(items) + logging.info("Finished loading %s items", len(items)) + else: logging.info("Adding %s items to table individually", feature_name) for item_attrs in items: logging.info("Item %s: %s", feature_id, item_attrs[feature_id]) hydrocron_table.add_data(**item_attrs) + + logging.info("Finished loading %s items", len(items)) diff --git a/hydrocron/db/schema.py b/hydrocron/db/schema.py index dd6f966..6dae601 100644 --- a/hydrocron/db/schema.py +++ b/hydrocron/db/schema.py @@ -115,11 +115,6 @@ def batch_fill_table(self, items): try: with table.batch_writer() as writer: for item in items: - logger.info( - "Item %s size: %s", - item[self.partition_key_name], - str(sys.getsizeof(item)) - ) if sys.getsizeof(item) < 300000: writer.put_item(Item=item) else: diff --git a/tests/test_data/api_query_results_csv.csv b/tests/test_data/api_query_results_csv.csv index 96b593a..ecda0f4 100644 --- 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